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2014

February 14th 2014: UK Scientists rank iMolview the best iPad/Android Molecular Viewer

iMolview came out on top in a recent comprehensive review of 12 molecule viewing apps for iPad and Android devices. The review article called "High-Quality Macromolecular Graphics on Mobile Devices: A Quick Starter.s Guide" was published in the Methods and Molecular Biology series by Drs. Yiu and Chen from King's College London, UK. Please click here to download the paper (subscription maybe required).

The article states that iMolview "tops the list because of its user friendliness and it offers the most complete set of functions for visual communication". The paper also includes a useful iMolview tutorial which takes you through the steps of importing molecules, coloring, transparency, surfaces, and exporting images.

You can download iMolview from the Google Play Store. or the Apple App Store.


February 5th 2014: MolSoft Releases New ICM Version 3.8

MolSoft is excited to release a new version of ICM. Please download the new version from www.molsoft.com/download.html. The Release Notes contain a complete list of new features and fixes but the key ones are listed below.

Graphics

  • Anaglyph 3D can be viewed using low cost 3D glasses and without any expensive 3D compatible hardware or monitors. It can be viewed directly on your computer's monitor, conference room projector, or on your iPad or android device. You can also print the image out rendered for viewing in 3D. Any red and cyan glasses will work well. [More Information] and [Documentation]
  • MolSkin MolSkin is a new macro that instantly makes publication quality graphics for surfaces and colors contact patches. [Documentation]
  • Movies from Slides A simple way to make a movie is by making a set of slides containing the scenes and then let ICM package them into a movie file. [Documentation]

Docking and Screening

  • SCARE The SCARE method allows you to take into account induced fit of the receptor upon ligand docking. The method systematically scans pairs of neighboring side-chains and replaces them with Alanine and docks a ligand to each of the "gapped" models. A full description of this method and validation is published here. [Documentation]
  • MolScreen is a set of high quality 2D fingerprint and 3D pharmacophore models for a broad range of pharmacology and toxicology targets. The models can be used for lead discovery or counter screening. The models use MolSoft's 2D QSAR/Fingerprint and 3D Atomic Property Fields ( Totrov 2008) methods. [More Information] and [Documentation]
  • Fragment Screening Screen a database of chemical fragments which are then ranked by p-value providing a quantitative measures of confidence that a fragment is a true active and binds in the specific pose in absolute terms, instead of just ranking it versus other fragments. [Documentation]
  • Docking directly from table The ability to dock directly from a loaded chemical table gives you some flexibility about which chemicals you wish to dock from a table and makes docking more interactive and more convenient. [Documentation]

New Data Search and Retrieval Options

  • Blast Search Now you can BLAST search the NCBI database directly in the ICM GUI. [Documentation]
  • Pocketome Search The Pocketome (www.pocketome.org) is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. [Documentation]
  • Drugbank Search The DrugBank (http://www.drugbank.ca/)database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. [Documentation]
  • UniProt Search The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. [Documentation]

Cheminformatics

  • Fingerprints Extended Connectivity Fingerprints (ECFP) have been added.
  • Chemical Search Chemical Search dialog allows to select an existing chemical table for Molcart or local search (see image).
  • InChI is now supported.
  • ToxScore A ToxScore function is now available in the Insert Column Dialog. [Documentation]
  • Atomic Property Fields A chemical table can now be clustered by Atomic Property Fields (see Chemistry/APF Tools}
  • Export to Excel The 2D chemical sketch is now exported to Excel. [Documentation]


January 24th 2014: Introducing MolScreen - A Panel of >360 High Quality Screening Models

MolScreen is a set of high quality 2D fingerprint and 3D pharmacophore models for a broad range of pharmacology and toxicology targets. The models can be used for lead discovery or counter screening. The models use MolSoft's 2D QSAR/Fingerprint and 3D Atomic Property Fields ( Totrov 2008 ) methods.

The models can be screened directly using MolSoft's ICM-Pro + VLS software. Alternatively we can screen a set of chemicals for you via our contract research services. Please contact us for more information about how to use MolScreen.


2013

December 19th 2013: Anaglyph 3D now available in ICM and iMolview.

MolSoft is excited to announce that Anaglyph 3D is now available to use in ICM and iMolview. Anaglyph 3D can be viewed using low cost 3D glasses and without any expensive 3D compatible hardware or monitors. It can be viewed directly on your computer's monitor, conference room projector, or on your iPad or android device. You can also print the image out rendered for viewing in 3D.

Here are the glasses the developers and scientists at MolSoft are using but any Red and Cyan 3D glasses will work.

To use Anaglyph 3D in ICM you will need the very latest version of ICM 3.7-3c and the documentation is here. Please contact us if you do not have the latest version yet. For mobile and tablet users please download the next iMolview update.


December 11th 2013: MolSoft ICM used in World's Largest Ever Virtual Screen Resulting in 3 New Lead Compounds.

At the recent Amazon Cloud Computing conference ( AWS Re:Invent ) scientists at Novartis reported using MolSoft's ICM-VLS in the largest ever virtual screen. MolSoft's software developers built a cloud-version of ICM-VLS which enabled Novartis to undertake this ground breaking achievement in cloud-based virtual screening. Cyclecomputing (a cloud vendor service company) enabled the jobs to be distributed to more than 30,000 cores in the USA and Europe. Novartis undertook 10.6 years of drug compound computations in 9 hours! The virtual screen resulted in three new lead compounds which are now being optimized by Novartis. This work was previously reported at MolSoft's user group meeting earlier this year and at BioIT 2012.

MolSoft's ICM-VLS has a strong track record of achieving high quality leads in ligand- and structure-based drug discovery. Please contact MolSoft if you would like to learn how you can undertake a similar screen.


August 29th 2013: MolSoft wins Competitive Bid to Work with AMG and TB Alliance on the Discovery of new TB Drugs.

MolSoft is excited to announce that they have won a competitive bid to work with AMG and TB Alliance on the development of vital new medicines that can be used to treat Tuberculosis (TB).

TB is a common disease which typically affects the lungs and if not treated correctly can be fatal. The current TB treatment is very long and can result in the patient not adhering to the strict regimen. With the recent approval of Bedaquiline as a treatment for multi-drug-resistant TB it gives hope that new and safe TB drugs can be identified.

In this collaboration, MolSoft will develop ligand-based models using published TB drug activity data as well as internal TB Alliance high throughput screening results. All work will be performed using MolSoft.s Internal Coordinate Mechanics (ICM) molecular modeling and cheminformatics software package which is used worldwide by academic and commercial laboratories. MolSoft will develop ICM 2D fingerprint and 3D Atomic Property Field (APF) models for each of the activity series. The 2D approach uses MolSoft.s proprietary method for generating hashed chemical fingerprints used in chemical search and similarity calculations. The 3D APF method, developed by Molsoft.s Principal Scientist Dr. Maxim Totrov, is a 3D pharmacophoric potential implemented on a continuously distributed grid which can be used for ligand docking and scoring.

Dr. Ruben Abagyan (MolSoft.s Founder and Professor at Skaggs School of Pharmacy and Pharmaceutical Sciences UCSD) says "The collaboration between chemists at TB Alliance and the scientific team at MolSoft represents an exciting application of their ICM ligand-based modeling and screening methods. MolSoft.s scaffold hopping technology is being used successfully in the pharmaceutical industry and it is a sign of this achievement that MolSoft was chosen to work on this project. I am confident that this alliance will give the best chance of identifying a new class of TB drugs."

Once the models have been prepared ICM-VLS will screen >12 million drug-like compounds to each model. High quality novel hits will then be chosen which are suitable according to the project.s pharmacokinetic and cytotoxicity criteria for hit to lead progression.


May 28th 2013: MolSoft Releases an HTML5 Molecular Editor

MolSoft announces the release of a HTML5 Molecular Editor which allows you to draw 2D chemical structure inside the web browser's page. It does not require any plug-ins (like Java) and works in any modern HTML5 compatible browser with Java Script enabled (including mobile platforms). You can sketch chemicals as well as import and export in MOL or SMILES format.

The editor is made available free of charge to academic institutions, please contact us if you wish to use it for commercial use. Please click here for more information on how to use the editor in your application.

To see the HTML5 Molecular Editor in action please visit one of our free popular online services.


May 27th 2013: New iMolview iPhone/iPad (v1.7) and Android (v1.2) Released

The biggest new addition to this version is the ability to read and contour electron density maps.

iMolview v1.7 iPhone/iPad

Tools/Load Electron Density Map

Loads electron density map from Uppsala EDS server (http://eds.mbc.uu.se/eds/). Once map is loaded you can toggle its display using 'Misc' panel in the main menu. In addition map can be contoured around selected atoms:

  • Select part of the molecule
  • Click on the contour icon in the 'Misc' panel on the pain menu.
  • Contouring level can be adjust using slider in the 'Tools' menu.

New icons in 'Misc' panel:

  • Map view toggle: [Optional] toggles display of the electron density map (if loaded). (See Tools sections to see how to load a map)
  • Map Contour toggle: [Optional] Contour density map around selected atoms. Contouring level can be adjusted in the Tools menu.

iMolview v1.2 Android

  • Load and contour electron density maps.
  • Tools/Measurement - This set of tools allows to measure distances, planar angles and torsions on displayed atoms. Tap on the tool you need and then sequentially select two,three or four atoms (depending on the measurement type).


April 19th 2013: iMolview v1.1 for Android Released

A new version of iMolview for Android has been released.

The key new features are: Release Version 1.1

  • Added molecular surface (skin) support
  • Added "Color Skin By Contact"
  • Added "Select Neighbors" button
  • Added "Select All" button
  • Option to color text sequence by 3D
  • Added Filter Selection by various properties
  • Added 'off line' information about PDB entry (References/Quick Info). (Note, that works only for newly loaded PDB objects)

April 6th 2013: Next generation of ICM desktop chemistry and biology modeling tools Workshop 2013

Thank you very much to all the participants of our workshop entitled "April 6th 2013: Next generation of ICM desktop chemistry and biology modeling tools Workshop 2013". It was an exciting workshop highlighting all the new features of ICM and a half day user group session. Please click here to view the contents of the meeting and the speaker abstracts.


2012

November 11th 2012: iMolview v1.6 Released

A new iMolview v1.6 has been released and is available on iPad. For more information about iMolview please see: http://molsoft.com/iMolview.html

The new features include:

  • Added interface to Dropbox (Documents/Dropbox)
  • Added molecular skin/surface representation
  • Added "Tools/Filter Selection" to adjust the current selection by various parameters
  • "Color Selection" can color individual representations.
  • ICM scripts embedded with the ICB file are available in the menu.
  • Added full screen mode.
  • Added interface to the ICM command language (Command tab in the search bar)
  • Tools menu (sbs stereo, measurements) appears for small molecules
  • 2D labels are displayed properly


October 5th 2012: MolSoft Releases an Android version of iMolView

MolSoft has released its popular iMolview mobile software for the Android today. Please download iMolview from the Android version from the Google Play Store..

About iMolview Explore the fascinating world of biological macromolecules: iMolview lets you browse and view in 3D protein and DNA structures from Protein Data Bank. Search for proteins like 'insulin' or 'thyroid receptor' in PDB or simply type pdb code the search bar. Information associated with each molecule in these databases is also at your fingertips. Sync and view your own structure files via iMolview folder on your sdcard. Molecular view can be customized with a rich set of molecular representations (wires, balls-and-sticks, space filling, ribbon diagrams, molecular surfaces) and various coloring schemes. Select residues, atoms or chains and color or change their representations individually. Select 'neighbors' of a ligand or any other selection to identify interacting atoms or residues. Set 'inertia' to the maximum and let your molecule spin in 3D indefinitely.


June 25th 2012: Fragment Based Drug Design using the 3D Ligand Editor

The ICM 3D Fully Interactive 3D Ligand Editor now contains tool which allows finding best scaffold replacement or linker fragment. It lets you interactively select two or more points of connection or replacement and search for possible fragments in the 3D database (SDF or Molsoft local database MOLT). The cutting bonds used to define scaffold are matched against a 3D database with a certain RMSD cutoff (usually very small). The best superposition is taken for the original compound and the chemical is minimized. The result is returned as a .standard. Ligand Editor hit list where results can be easily browsed, sorted and compared. Linker prediction can be made in the presence or absence of the receptor. Filters such as energy strain, maximum number of rotatable bonds and contact distance to the receptor can be used. More documentation for this tool can be found here.


June 7th 2012: iMolview Version 1.5 Released

iMolview is an app for the iPhone/iPad that lets you browse protein, DNA, chemicals, and molecular documents in 3D. We have released a new version of iMolview (v1.5), which includes support for high resolution retina display, simultaneous display of multiple proteins and superposition, side-by-side stereo, and tools for measuring and displaying distances and angles. The app costs 99 cents and can be downloaded from iTunes. Please click here for more information.


June 5th 2012: New version of ActiveICM released.

A new ActiveICM download is available, please click here. We recommend that all users upgrade to the latest version. The new version fixes a bug that reported the error message .[588] too many different atom radii problem.. Please download the latest version now. ActiveICM is a free plugin that enables you to view and display 3D ICM graphical slides and animations interactively inside Microsoft PowerPoint and web browsers such as Internet Explorer, Safari and Mozilla Firefox. The files can be prepared and saved in ICM Browser, ICM Browser Pro or ICM Pro. ActiveICM is being used for scientific publishing by journals such as PLoS ONE and Nature.


May 9th 2012: Impressive ICM Docking and Screening Benchmark Published

Last year scientists at MolSoft (Max Totrov Ph.D.) and UCSD (Ruben Abagyan Ph.D. and Marco Neves Ph.D.) competed in an industry-wide docking and screening competition organized by OpenEye, Merck, and GSK. Two challenges were set:

Pose Prediction

  • Docking, extended Astex set: 85 targets and 170 docking poses
  • Initial ligand conformations provided

Virtual Screening Recognition

  • VLS recognition: the DUD set (Useful Decoys)
  • 40 targets, 10,000 decoys for each

MolSoft ICM achieved excellent results in both challenges ranking in first place in both challenges. ICM-Pro docking gave pose prediction results of < 1A top 1 pose: 78% of cases and < 2A top 1 pose: 91% of cases. For virtual screening, median area under ROC curves equal to 69% and 82% were achieved. A full description of the data analysis can be read here


April 4th 2012: User Group Meeting 2012 . Thank you to everyone who participated!

Everyone at MolSoft would like to thank all those who attended the ICM User Group Meeting this year. Thanks to all the great speakers for their excellent presentations. We had an interesting and enjoyable time which included talks on a wide range of topics including: Protein Structure Analyis, Membrane Protein Modeling, Modeling Immune Response Proteins, Latest ICM Developments, Chemical Biology and Cheminformatics, ICM for Teaching and Communication, Protein-Protein Docking, and Lead Discovery. Click on the links below to see what we all got up to - it was not all just science!

UGM 2012 Links

Meeting Program

Photos by Dr.Polo Lam - MolSoft and Photos by Eugene Raush - MolSoft


March 7th 2012: ICM Version 3.7-2c Released

MolSoft is excited to announce the release of ICM version 3.7-2c. The new version can be downloaded from our support site here. The key new features are described below but for a detailed list please see the release notes.

Atomic Property Fields APF is a 3D pharmacophoric potential implemented on a grid (Totrov 2008 and 2011 ). APF can be generated from one or multiple ligands and seven properties are assigned from empiric physico-chemical components (hydrogen bond donors, acceptors, Sp2 hybridization, lipophilicity, size, electropositive/negative and charge). An independent study found that APF is most accurate method for chemical superposition and ligand-based 3D virtual screening compared to several other commercial and academic softwares. (Giganti et al 2010).

  • Ligand based screening using APF [more..]
  • Calculate pairwise APF scores [more..]
  • Generate a consensus pharmacophore [more..]
  • Superimpose ligand binding sites by Atomic Property Fields [more..]

3D ligand Editor The ligand editor is a powerful tool for the interactive design of new lead compounds in 3D. It allows you to make modifications to the ligand and see the affect of the modification on the ligand binding energy and interaction with the receptor.

  • Multiple Receptor Docking in the 3D ligand editor [more..]
  • Chemical fragment linking in the 3D ligand editor [more..]
  • Dock to APF fields in the 3D ligand editor [more..]

Protein Modeling Inside ICM there are many features for homology modeling and loop modeling. This new option can be used if you have a gap in your protein and you want to find loops in the PDB which fit the gap.

  • New protein loop design method is now available. [more..]

Chemisty A couple of new options in the Chemistry menu.

  • Calculate ligand strain [more..]
  • Calculate ligand entropy [more..]

"Pipe-able" Scripting in ICM New options to pipe icm commands and scripts.

  • Easy way to write pipe-able scripts (see $ICMHOME/molpipe/*.icm).
  • Easy way to add parallelism to unix/mac ICM scripts: fork with pipe option ($ICMHOME\molpipe\*.icm)

Other New Features and Options

  • Desciption of all the fields in the docking .tab file [more..]
  • Easy manipulation of internal coordinates copy/paste and drag'n'drop between icm sessions ( images, molecular objects, meshes, tables ) [more..]


February 8th 2012: Latest ICM Newsletter Available for Download

Please see our latest newsletter (PDF Format) with information on:

  • Ligand-Based Screening Using Atomic Property Fields (APF)
  • Multiple Receptor Docking in the 3D Ligand Editor
  • Atomic Property Fields Docking in the 3D Ligand Editor
  • Virtual Ligand Screening (VLS) Result Analysis Tools
  • New VLS Hitlist Visualization Options
  • New High Precision Loop Modeling Tutorial
  • Details about our 2012 ICM User Group Meeting in March


2011

September 13th 2011: New iMolview Version Released - Now with Slides!

Today MolSoft released a new version (v1.4) of its popular molecular viewing app called iMolview for the iPad and iPhone. The new features include the ability to save molecular documents which include structure and slides. A slide is a combination of a view point and graphics representation. In iMolview you can create multiple slides and access them later after the document was saved.

To create a slide:

  • Setup a view and representations (color, label, etc.)
  • Go to Menu/Slides and choose "Save Current View"
  • Give a name and press 'OK'. It should appear in the list
  • Repeat these steps to create more slides

To switch between slides you may use Menu/Slides or arrows on the sides of the center button. After all slides are done you need to save your molecular document. Goto Menu/Documents/Save Current Document and give it a name. The document will be saved into History folder and can be loaded later. This file can also be copied to your PC,MAC or Linux and opened with free ICM-Browser, or you can embed this document as a live 3D object into web page using ActiveICM technology.

iMolview costs only 99cents and is available via the Apple App Store. Please send us your feedback on the new version and rate the app at the Apple app store.


September 6th 2011: MolSoft's ICM Modeling Software Correctly Predicts Agonist GPCR Structure

A couple of years ago scientists using MolSoft's ICM software predicted and published the agonist bound structures of beta-adrenergic and adenosine A(2A) GPCR receptors. The accuracy of these models were confirmed by recently published x-ray crystal structures of these GPCRs. This work is summarized in a recent paper in Trends in Pharmacological Sciences. This work highlights the power of MolSoft's ICM modeling softare for the development of new ligands for GPCRs and also the use of these models for other pharmacological and biochemical studies.


September 1st 2011: Explore the Pocketome using ActiveICM

Prof. Abagyan's lab at UCSD have developed a website called the Pocketome which is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. The pocketome ensembles are generated from UniProt and PDB and clusters and validates the binding pockets based on the consistency of the composition between multiple structures. The pockets can then be viewed using ActiveICM or downloaded and viewed using ICM-Browser.


August 10th 2011: GPCR Dock 2010 evaluation undertaken using MolSoft's ICM and ActiveICM tools.

SummaryThe community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule antagonists and CXCR4 with a synthetic cyclopeptide. Thirty-five groups submitted their receptor-ligand complex structure predictions prior to the release of the crystallographic coordinates. With closely related homology modeling templates, as for dopamine D3 receptor, and with incorporation of biochemical and QSAR data, modern computational techniques predicted complex details with accuracy approaching experimental. In contrast, CXCR4 complexes that had less-characterized interactions and only distant homology to the known GPCR structures still remained very challenging. The assessment results provide guidance for modeling and crystallographic communities in method development and target selection for further expansion of the structural coverage of the GPCR universe.


July 7th 2011: New Method to Visualize Protein Mutations Using ActiveICM

This month the Journal of Inherited Metablic Disease published a fully interactive 3D research paper using MolSoft's ActiveICM. The paper describes the crystal structure of human fumarate hydratase along with mutations that are mapped onto the 3D structure. The reader can click on a mutation or group of mutations and the fully interactive 3D display takes the reader to the location in the crystal structure in 3D. The reader can then interact (zoom, rotate etc..) with the molecule making the it easier to visualize the data. You can read more on the SGC website here.

June 17th 2011: iMolview gets reviewed on popular crystallography blog and store website P212121.com

We were excited to read a review of MolSoft's iMolview app for iPad and iPhone on the popular crystallography P212121.com website. Click here to read it... The P212121.com website is not only a blog but also a macromolecular crystallography equipment and reagent store. Scientists can browse thousands of products from dozens of companies all from a single website, this not only saves you time but you also avoid the sales reps! The iMolview app is being used around the world by scientists in many disciplines and we have received many positive reviews. The app is under active development, so if you are a user and there is a feature you would like to see please contact us. If you have not tried iMoview yet you can do so by purchasing it from the apple store for only 99 cents.


May 17th 2011: iMolview Version 1.2 Released

New in Version 1.2:

  • issue with older iPhone/iPod devices FIXED
  • structure files (pdb/icb) sync via iTunes
  • download history
  • easy toggle of individual molecule display via sequence view tabs
  • faster refresh in CPK representation
  • display tools popup bar on selection
  • improved handling of very large structures
  • neighbors in other chains selection, such as atoms in the vicinity of selected ligand
  • external links menu: Uniprot and RCSB entries in addition to PubMed
  • atom type coloring for hetero-atoms only - allows combining chain-specific colors and atom type color coding
  • 3D residue picking is now tracked in sequence view
  • easy clear display button (X)
  • bug/crashes fixes


May 5th 2011: MolSoft releases iMolview for the iPhone and iPad

iMolview is an app for the iPhone and iPad that lets you browse protein, DNA, and drug molecules in 3D. The app has a direct link to the Protein Data Bank (PDB) and DrugBank and has a fast and easy to use interface. Touching the molecules via the screen allows you to interact immediately with the 3D structures in a unique way. You can zoom in and out, rotate, spin, pan, and clip the 3D molecules with your finger tips in ways that are impossible using a traditional mouse and desktop computer. iMolView allows you to search for drugs such as 'ibuprofen' or 'gefitinib' in DrugBank, or proteins like 'insulin' or 'thyroid receptor' in the PDB and immediately explore their structure and annotation. This handy app allows you to quickly and easily view and interact with 3D molecules anywhere and at any time whether you are at the bench, at a conference, or just having coffee with colleagues!

May 5th 2011: Watch a Lecture by MolSoft's Principal Scientist Max Totrov Ph.D. about Ligand Binding Site Superposition and Comparison based on Atomic Property Fields

Max Totrov (Principal Scientist, MolSoft LLC) recently gave a lecture in Korea on "Ligand Binding Site Superposition and Comparison based on Atomic Property Fields". You can watch the lecture here and read more about this in this published paper.

February 2nd 2011: MolSoft awarded a patent for its ActiveICM Technology

MolSoft LLC were today awarded a patent entitled "Structured documents and systems, methods and computer programs for creating, producing and displaying three dimensional objects and other related information in those structured documents" for its ActievICM technology (US Patent Number 7,880,738). The patent is for a structured document file which includes graphical and non graphical information. The graphical information includes the vector and coordinate description of a representation of at least one three dimensional object and at least one of the following group of view attributes or features: rotation, translation, view angle, lighting, colors, specific graphical representations, labels and parameters. The vector and coordinate description are stored with or independently from the one or more view attributes or features and the vector and coordinate description and the one or more view attributes are stored in a single file which can be accessed and viewed by a structured document viewer. Related authoring tools and viewers are also disclosed.


February 1st 2011: First paper published in Nature Structural and Molecular Biology using ActiveICM

Nature Structural and Molecular Biology is now using using MolSoft's ActiveICM technology. The first paper published in this enhanced format in Nature Structural and Molecular Biology can be viewed here. Thank you to the Editors at Nature, the authors of the paper, and Dr. Brian Marsden and Dr. Wen Hwa Lee at SGC for their support and for making this possible. ActiveICM is developed by MolSoft and allows you to view fully-interactive 3D molecules and animations on the web or PowerPoint.

Dr. Ruben Abagyan who is Molsoft's founder and Professor at the Skaggs School of Pharmacy at UC San Diego said, "It is great to see ICM and its derivative, activeICM, revolutionizing the way scientific information is communicated to the public. Since their creation 20 and 6 years ago respectively we managed to transform this software into a sophisticated multi-platform environment. We are committed to the continuous development of this platform and making it freely available for the research community."

To view the ActiveICM content:

  • Display the HTML version of the paper in a web browser.
  • Download the ActiveICM plugin here or click on the link provided by Nature Structure and Molecular Biology (Image 1 and 2 below). If you click on the Enhanced Article link in the paper this will give you information on how to download the ActiveICM plugin..
  • Click on the hyperlinks in the html version of the paper and a popup ActiveICM window will be displayed (Image 3 below).
  • Use your left mouse button to rotate the molecule(s), zoom in by clicking on the left hand side of the display (Image 4 below).
  • Click on the MolSoft logo (bottom right corner) for more options.


(1) (2) (3) (4)

You can make similar files using the free ICM-Browser http://www.molsoft.com/icm_browser.html


January 12th 2011: MolSoft develops ChemDiv's Online Chemical Store

MolSoft recently developed ChemDiv's new eShop containing the world's largest small molecule inventory. The eShopuses MolSoft's proprietary cheminformatics tools to enable you to search the database by sketching the structure or part of a structure, by ID number, SMILES, or by chemical files such as Mol and SDF. A template structure can also be used to build libraries based around a particular substructure. There are also chemical property filtering tools available such as MW, logP, and Number of rotatable bonds, hydrogen bond donors and acceptors.


January 4th 2011: MolSoft Releases Major New ICM Version (v.3.7)

MolSoft is excited to announce the release of ICM v3.7-2 which is a major new version upgrade with many new features and an updated user interface. You can download the latest version at our support site. Click here for more information on the new features available in ICM v 3.7.

New feature hightlights include:

  • New ICM force field.
  • New easy to use HTML editor for creating molecular documents.
  • WebKit integration into ICM.
  • Charge protonation state prediction using a pKa model.
  • Explicit group docking.
  • Implicit membrane models.
  • And much more...


2010


November 15th 2010: MolSoft Scientists Develop New ICM Force Field

Scientists at MolSoft have developed a new physics-based internal coordinate mechanices force field. Please see the publication in the Proteins journal by Arnautova et al where the force-field has been applied to protein loop modeling. The new force-field contains new parametization for the dielectric constant, an improved hydrogen bond determination method, and implementation of novel backbone atom torsional potentials which include bond anlges of the carbon (alpha) atoms into the internal variable set.

Follow these instructions to use the new force field in your own scripts for energy minimization and optimization. If you are interested in modeling loops you can use the _loopmodel macro where all these parameters are already pre-set.

  • Use ICM version 3.7-2a. This can be downloaded by logging into our support site.
  • The polypeptide must be built or converted with the icmff residue library to do this:
    
    LIBRARY.res = {"icmff"}
    read library
    
  • The dielectric constant should be set to 2.
    
    dielConst = 2. 
    
  • In addition to regular energy terms, "bb" must be turned on
    
    set term "bb" 
    
  • The force-field method should be set to icmff
    
    ffMethod = 4 
    


October 29th 2010: MolSoft LLC has moved office location.

After more than 10 years at Torrey Pines Court in La Jolla, MolSoft has moved to larger custom designed offices in Sorrento Valley. From the 1st November our new address will be: 11199 Sorrento Valley Road, S.209, San Diego CA 92121


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September 7th 2010: Dr. Brian Marsden (SGC Oxford) to Present iSee at Bio-IT World Conference

The development of ActiveICM otherwise known as iSee has been a result of a strong collaboration between scientists at the SGC and developers at MolSoft. If you are attending the Bio-IT World Conference in Hannover next month please be sure to attend the talk by Dr. Brian Marsden from the SGC entitled "iSee - Dissemination of Structural Biology Data to the Masses". The talk will be at 11:30AM on Wednesday 6th October in the IT Infrastructure and Informatics session,please click here to read the abstract for his talk.


August 1st 2010: Molecular and Cellular Proteomics Journal Now Accepting Publications Using MolSoft's ActiveICM Technology

Following on from the success PLoS ONE and PLoS Biology have had using ActiveICM it gives us great pleasure to let you know that the Molecular and Cellular Proteomics Journal, published by the American Society for Biochemistry and Molecular Biology (ASBMB) are now accepting articles in ActiveICM format. Two articles have been published in this format already. Please click on the link below to view them. Remember to download the free ActiveICM plugin to view them.

John H. Morris, Elaine C. Meng and Thomas E. Ferrin (2010) Computational Tools for the Interactive Exploration of Proteomic and Structural DataAugust 1, 2010 Molecular & Cellular Proteomics, 9, 1703-1715. : doi: 10.1074/mcp.R000007-MCP201

Keren Lasker, Jeremy L. Phillips, Daniel Russel, Javier Velazquez-Muriel, Dina Schneidman-Duhovny, Elina Tjioe, Ben Webb, Avner Schlessinger and Andrej Sali (2010) Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data August 1, 2010 Molecular & Cellular Proteomics,9,1689-1702. doi: 10.1074/mcp.R110.000067


July 29th 2010: MolSoft's Fully Interactive 3D Molecule Technology is Now Being Used by the PLoS Biology Journal

Click to enlarge image.

This week PLoS Biology have started using MolSoft's ActiveICM software to publish fully interactive 3D papers. This is following on from the recent success of the series in PLoS ONE. The articles allow the user to rotate, translate, and zoom 3D structures whilst reading the scientific paper and view animations directly linked to hyperlinked text. The publication of these papers is due to a collaboration between MolSoft and the SGC. Click on the links below and then choose Enhanced Version to view the latest papers in this fully interactive 3D format. You will need to download ActiveICM to view them.

Rellos P, Pike ACW, Niesen FH, Salah E, Lee WH, et al. (2010) Structure of the CaMKIIG/Calmodulin Complex Reveals the Molecular Mechanism of CaMKII Kinase Activation.PLoS Biol 8(7): e1000426. doi:10.1371/journal.pbio.1000426

Davis TL, Walker JR, Campagna-Slater V, Finerty PJ Jr, Paramanathan R, et al. (2010) Structural and Biochemical Characterization of the Human Cyclophilin Family of Peptidyl-Prolyl I somerases.PLoS Biol 8(7): e1000439. doi:10.1371/journal.pbio.1000439

July 26th 2010: ICM-Pro Peptide Design Success Story: Design of a V3 HIV-1 gp120 mimotope.

In the current issue of Nature Structural and Molecular Biology scientists at New York University and MolSoft have reported the identification of conserved structural elements in the V3 crown of HIV-1 gp120 which could serve as epitopes to be targeted by a vaccine against HIV-1. A cyclic V3 mimotope peptide was designed using MolSoft's ICM-Pro by inserting a disulfide bond and four residue linkers between the preserved N and C terminals of V3. The peptide was designed by searching the Protein Databank for polypeptide segments that would match the ends of the V3 strands and the stability and positioning of the disulfide bridge were selected by energy minimization. The resulting mimotope was shown to interact with mAbs 1006, 2219 and 2557. The predicted structure and interactions of the mimotope were confirmed by X-Ray crystallography. This mimotope can potentially be used to design immunogens that could induce antibodies to V3 and other variable regions of gp120.


June 17th 2010: MolSoft's ICM Software Excels in Published Virtual Ligand Screening Comparison

In a recent publication by Giganti et al (Pasteur Institute, France) in the Journal of Chemical Information and Modeling ICM displayed the best performance in terms of molecular alignment and docking accuracy compared to four other software programs. The authors acknowledge the efficiency of MolSoft's Biased Probability Monte Carlo method which is good at sampling flexibility. You can read about the comparison here. The authors tested ICM-docking and the Atomic Property Field (APF) method. The APF method is described here: Totrov M (2008) Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. Chem Biol Drug Des 71: 15-27


May 28th 2010: MolSoft's Virtual Screening Software Discovers New Potent Selective Inhibitor for p300 Histone Acetyltransferase

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A collaboration between scientists at MolSoft and the John Hopkins University has resulted in the discovery of a potent selective small molecule inhibitor of p300/CBP Histone Acetyltransferase (P300 HAT). MolSoft scientists screened ~500K molecules using ICM-VLS and selected 194 for testing which resulted in 30 active compounds. P300 HAT is a transciptional activator implicated in many gene regulatory pathways and protein acetylation and is an important anticancer target. Read more here in the article published in Chemistry and Biology.


April 30th 2010:MolSoft's ICM Molecular Graphics in New Crystallography Textbook

MolSoft's ICM-Browser-Pro software was used to make all the molecular graphics images in Dr. Bernhard Rupp's new book called "Biomolecular Crystallography: Principles, Practice, and Applications to Structural Biology" published by Garland Science. To find out more about the book please click here and to read a review of the book please see this article in Acta Crystallographica Section D.


March 31st 2010: MolSoft Awarded New NIH Grant for a Glycosylation Modeling System for Internal Coordinate Mechanics

MolSoft has been awarded an NIH grant to work on developing a Glycoprotein modeling system for internal coordinate mechanics. The 2 year project will develop an extension to the current force-field (ECEPP) and a library of common glycosylatting chemicals for the modeling and docking of glycan-binding proteins. Glycans are key molecules in the immune system, cancer progression and cell-cell recognition and the ability to model them accurately is important for structure based drug design. You can read more about the aims of the grant here.


March 3rd 2010: Recent ICM Publications.

Please see some recent ICM publications including identification of new G-Protein Coupled Receptor (GPCR) antagonists using ICM-VLS (Katritch et al J. Med Chem 2010) and the modeling of the interactions of a Class B GPCR with its ligand using experimental restraints (Dong et al 2010). Another interesting paper by Rueda et al describes methods for the selection of experimental protein conformations for virtual screening.


2009


12.23.2009: End of Year Update

Below we have some end of year ICM news and a round up of some of our 2009 success stories.

MolSoft in the Media

Last month the San Diego Union Tribune wrote an article about MolSoft - you can read the article online here. In July the American Chemical Society publication Chemical and Engineering News also reported on our ICM 3D Ligand Editor. There was also a lot of interest by blog writers and other media outlets about MolSoft's ActiveICM being used by PLoS ONE and SGC scientists for the publication of fully interactive 3D scientific papers. SGC scientists refer to ActiveICM as iSee and they have summarized all the media interest in this development here in the whatisisee wiki.

Upcoming Workshops

This year we held two sold out ICM workshops and an ICM User Group Meeting. The User Group meeting was a fun and scientifically rewarding experience. You can see some of the photos from the User Group Meeting here (Photos by Dr. Lars Brive - Goteburg). Please join us in 2010 at one of our 2010 workshops including an ICM Scripting Workshop in January - places are filling up quickly so please register as soon as possible.

  • Jan 21st-22nd, 2010: ICM Scripting Workshop. La Jolla CA
  • Apr 29th-30th, 2010: ICM Workshop:Protein Structure and Drug Discovery. La Jolla CA.
  • Oct 7th-8th, 2010: ICM Workshop:Protein Structure and Drug Discovery. La Jolla CA.
More information here

Bringing Online Publications to Life

As mentioned earlier one of the big events this year was the exciting use of ActiveICM in the PLoS ONE journal to display fully interactive 3D objects. For the first time fully interactive 3D molecules were embedded in a peer-reviewed collection of research papers due to a collaboration with scientists at the SGC in Oxford UK. You can see the full PLoS ONE collection on their website. You can use ActiveICM for free and download it from here.

Lots of New Cheminformatics Features

During the past year the number of chemistry related features inlcuded in ICM has grown significantly. We now have two chemistry products ICM-Chemist and ICM-Chemist-Pro. ICM-Chemist is ideal for all 2D chemical operations including sketching, editing, clustering and database enumeration. ICM-Chemist-Pro includes all the tools in ICM-Chemist plus 3D options such as chemical superposition and our popular 3D ligand editor. If you would like to try these products please let us know and we can send you an evaluation license.

New ICM-Chemist Tutorials Including Videos

Please check out the new series of ICM-Chemist tutorials including online videos. If you have ICM-Chemist or ICM-Pro-VLS then you have all the features described in these tutorials. More tutorials in this format will be released early next year so we would welcome your feedback.

Holiday Reading! Some Selected 2009 ICM Success Stories


10.20.2009: MolSoft's New Technology Brings Online Publications to Life in Fully Interactive 3D.

Scientific publishing is now going 3D. For the first time in online publishing history, the PLoS ONE journal is publishing original research papers containing fully annotated and interactive 3D objects. This 3D environment provides a "movie-like" experience but with a significant difference - the reader is in control of the scenes and each view is linked directly to the text. This is possible because of a new technology called ActiveICM developed by MolSoft LLC. ActiveICM is now being used for scientific publishing due to a collaboration with scientists at the SGC. Initially the technology is being applied to the life sciences for the 3D display of the atomic structures of molecules implicated in disease. ActiveICM can also be used for any online publication where a 3D view would enhance the subject matter. Click here to see the PLoS ONE collection of papers. Click here to read the press release.


10.08.2009: New MAC version of MolSoft's ICM Desktop Modeling Software is Now Available

Please visit our support site to download the latest MAC version 3.7-1f of ICM-Browser, ICM-Browser-Pro, ICM-Chemist and ICM.


10.07.2009: MolCart Building Blocks Database for Combinatorial Chemistry has been Updated

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The MolCart Building Block database has been updated. The database consists of chemical building blocks for combinatorial chemistry from 32 different chemical vendors and contains 4,408,865 non-redundant chemical fragments. The database contains a wide variety of scaffolds which can be used to generate libraries using Molsoft's combinatorial library tools contained in ICM-Chemist. ICM-Chemist contains a large selection of tools for chemical enumeration and decomposition. You can create or modify a Markush structure and enumerate a library on the fly by adding chemical fragments to defined "R-groups". You can also enumerate by chemical reaction and decompose a database into chemical fragments.


9.22.2009: A new 64-Bit Beta Version of ICM is now available

A new 64-bit Beta version of ICM is available. Please contact andyATmolsoft.com if you would like to try this version of ICM.


9.19.2009: ICM Graphics On Front Cover of New Book on Chemogenomics

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ICM graphics is featured on the front cover of a new book edited by Edgar Jacoby (Novartis) on Chemogenomics. More information about the book can be found here. The image is of the contoured electron density of a ligand. Click here for instructions on how to contour electron density in ICM.


7.22.2009: Updated MolCart Compound Database

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The Molcart Compound Screening Database has been updated. The database is a collection of compounds from 33 chemical vendors who let us know whenever a new set of compounds is added or removed from their database.The database currently contains 8,275,223 compounds and the total number of redundant compounds is 4,474,597. The latest changes to the database are documented here. One of the advantages of the MolCart Compound Screening Database is that we take great care to ensure the compounds that are listed are actually available for purchase. Other compound database collections list compounds that are virtual and in theory can be synthesized but they are expensive and are rarely available for quick purchase. If you are a MolCart customer please update your database collection by clicking here and download individual vendor databases or our non-redundant compilation. If you are interested in purchasing MolCart you can get a 2 week trial license by contacting us at info@molsoft.com.


6.25.2009 Press Release San Diego, CA: Interactive Drug Design with the ICM 3D Ligand Editor

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MolSoft LLC (www.molsoft.com) is a leading developer of breakthrough technologies in computational biology and chemistry. MolSoft has officially released a new ground-breaking tool for the interactive, three-dimensional (3D) design and docking of new drug candidates. The ICM Interactive 3D Ligand Editor is an easy-to-use desktop application that allows a chemist to visualize a receptor-ligand complex and then apply their experience and intuition to explore, design and optimize new drug-like compounds. Recently, this tool was validated in a community-wide evaluation of modeling and docking software where ICM performed very successfully in predicting the pose of a ligand to a G-Protein Coupled Receptor (see Michino et al Nature Reviews Drug Discovery 8: 455-456).

A common scenario in drug design is that a lead compound binds reasonably well to a target protein and the ligand-receptor interactions are known, but the problem of how to improve the binding properties, synthetic feasibility, and metabolic-physicochemical properties of the ligand remains. This is where the power of the ICM 3D Ligand Editor comes in: it allows the chemist to see the ligand-receptor interactions clearly on the computer screen. Chemists can simply explore their new ideas with a click of a mouse in a fully interactive and intuitive 3D environment. The effect of a change to the ligand in terms of its interaction with the receptor is immediately displayed on the screen for the chemist's immediate evaluation.

The pharmaceutical industry is already a major user of MolSoft's ICM 3D Ligand Editor technology and industry feedback has enabled MolSoft's developers to build a tool suited for chemists working in drug discovery research. Dr. Eric Martin, Director of Computational Chemistry at the Novartis Institute for Biomedical Research says "The ICM ligand editor is an extremely effective drug design tool for interactively merging the rigor of complex molecular calculations with the intuition of experienced medicinal chemists. We use it extensively both 1-on-1 at the graphics workstation, and in team meetings using a 3D projection system".

So how do you use the ICM 3D Ligand Editor? The process is simple and designed to make life easier for the chemist. First, the ICM 3D Ligand Editor displays the crystal structure or model of the receptor-ligand complex along with the properties of the pocket, ligand solvent accessible surface, ligand strain or unsatisfied hydrogen bonds. The chemist can then start exploring ideas for improving the ligand by selecting a new chemical group and adding it to the ligand. The binding energy and interaction with the receptor is immediately assessed and displayed on the screen. The chemist has access to a full panel of chemical groups, linkers, bond types, stereo/isomer options and atom selections, which can be used to quickly try many different ideas. Importantly, should something be undesirable, a key feature allows the chemist to quickly undo changes to the ligand with a single mouse click and get back to the original ligand. Once the chemist has designed a ligand they are happy with, it can be saved in a single file to share with colleagues. The editor is a perfect tool for communication among scientists and can aid brain-storming session in an exciting way because hypotheses can be tested instantaneously.

The ligand editor has many advanced functions that make use of MolSoft's much acclaimed ICM technology, which is the backbone of the tool. Inside the editor, features such as ligand minimization, docking, atom tethering and virtual screening are available to use. For example, thousands of chemical groups can be screened on a particular point of the ligand resulting in a ranked list of complexes. The editor can also be used for fragment based drug design and optimization. According to Professor Ruben Abagyan, MolSoft Founder and professor at the Scripps Research Institute, "This new interactive environment for lead discovery combines the best practices in flexible docking and interactive modeling. The user-friendly environment changes the way chemical probes are discovered in industry and academia. Furthermore, the freely available ICM Browser and ActiveICM plugin allow scientists to disseminate data among chemists and biologists in an interactive way."

The ICM 3D Ligand Editor is part of the ICM-Chemist-Pro software product available from MolSoft LLC (www.molsoft.com).


6.4.2009 New Feature: Display Alignment Profile

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A popular request from the biologists who use ICM is to develop a way to visualize sequence conservation in an alignment. Therefore in ICM version 3.6-1e (to be released soon) we have developed a way to display the sequence profile in a multiple sequence alignment. The consensus strength of a residue at a point in the alignment is visually represented by the size of the letter in the profile (see accompanying image).

To display the sequence profile:

  • Make a multiple sequence alignment.
  • Click on the icon in the alignment to display the alignment options tool panel.
  • Check the profile option.


5.29.2009 MolSoft's ICM delivers star performance in GPCR modeling and docking competition.

Modeling structures of G Protein Coupled Receptors (GPCRs), the most prevalent drug targets, has always been a great challenge. Predicting how and where the drugs bind to those receptors is an even greater challenge. Until recently only bovine rhodopsin and beta 2 adrenergic receptor structures have been solved. Yet, when the structure of the Adenosin receptor A2a (the receptor for caffeine) was solved in a complex with a drug, the crystallographers annouced a challenge for all modellers and dockers to predict the binding interactions of the drug with the receptor.

60 groups have registered for the competition and 29 dared to submit their models. Up to 10 models were allowed to be submitted. More importantly the models were supposed to be ranked since usually only the top predicted pose is further pursued.

In a recent paper by Michino et al published in Nature Reviews the results are published (click here to read the paper). Two teams from Molsoft, Katrich-Abagyan and Lam-Abagyan built the models that had the largest number of correct ligand-receptor interatomic contacts, 45 and 34 out of 70, respecitvely out of all participants. Moreover, both models were ranked number 1, while the prediction from a competing modeler thathad better drug RMSD (when a flexible drug ring was considered) was only ranked 2. The fourth model from the Baker/Rosetta group had only 18 of correct contacts and this pose was only ranked 4th.

The ICM-based GPCR modeling approach employs the Ligand-guided principle and the ICM global optimization algorithm, and its success in ligand docking shows applicability of the method to a large class of problems in the field of GPCR drug discovery.


5.15.2009 New Feature: Accent Graphics

A new edge accent feature is available in icm version 3.6-1e which will allow you to make images as shown in the pictures below.

The option can be activated in the command line using:


GRAPHICS.sketchAccents = yes

Click on the images below:


5.10.2009 Pictures from the 2009 ICM User Group Meeting

Picture by: Dr.Lars Brive (Goteborg University)

Thank you to everyone who attended the ICM User Group Meeting last month. It was a really enjoyable meeting with some great presentations. Click here to view the meeting program with speaker abstracts and bio.

Thank you to Dr. Lars Brive (Goteborg University) for his photos of the lunch at the beach (small/large) and also to Prof. Bengt Persson (Linköping University & Karolinska Institute) whose photos can be viewed here:

ICM User Group Meeting - Photos Provided by Prof. Persson


4.16.2009 Breaking News: Scientists identify compounds using MolSoft's ICM-VLS that might fight bird flu.

MolSoft's ICM-VLS was used by scientists in Canada and Hong Kong to screen the NCI ligand database to identify a synthetic compound which appears to be able to stop the replication of the influenza viruses, including bird flu virus. See the paper at J Med Chem webiste and here at MSNBC.


4.14.2009: MoSoft and Virginia Tech are awarded NIH grant to develop a new class of resistance-breaking insecticides to reduce malaria transmission.

Researchers from Virginia Tech and Molsoft LLC have received a five-year, $3.557 million grant from the National Institute of Allergy and Infectious Diseases (NIAID) to continue their promising work on a new class of resistance-breaking insecticides to reduce malaria transmission. Click here for the full story.


2.1.2009 ICM-Browser-Pro Image on Front Cover of Parasitology Journal

Thank you to Dr. Kandeel at Gifu University in Japan who let us know that one of the images from his paper in Parasitology was included on the front cover of the January issue of Parasitology. The image was made in ICM-Browser-Pro, see the front cover here.


2008


December 2008 Newsletter

MolSoft Newsletter: December 2008 In this issue:

  • End of Year Discount
  • Next ICM Workshop: Protein Structure and Drug Design February 5th to 6th 2009
  • 2009 ICM User Group Meeting: Challenges in Protein Structure Prediction and Drug Design
  • New ICM Publication: Type-II Kinase Inhibitor Docking, Screening, and Profiling Using Modified Structures of Active Kinase States
  • Floating ICM licenses for the Mac are now available.
  • New Features in the latest ICM version 3.6-1d.
  • ICM Power Tip: How to search for chemicals in very large databases.

End of Year Discount

We are offering a 20% discount on all ICM-Pro and MolCart products. This special end of year offer applies to new customers or current customers who wish to add additional licenses to their existing license agreement. Submit your purchase order before December 31st 2008 and receive a additional 20% discount on all our ICM-Pro molecular modeling and cheminformatics products.

Next ICM Workshop: Protein Structure and Drug Design February 5th to 6th 2009

The workshop will be conducted by: Prof. Ruben Abagyan (The Scripps Research Institute) and Dr. Maxim Totrov (Principal Scientist, MolSoft LLC). The workshop will consist of lectures, demonstrations, and "hands-on" computational experiments and cover the following topics:
  • Sequence and Protein Structure Analysis
  • Protein Modeling and Simulations
  • Structure Validation and Optimization
  • Ligand Binding Site Prediction
  • Small Molecule Docking and Virtual Ligand Screening
  • Structure-based development of target-specific compound libraries
  • Cheminformatics, chemical clustering, searching, superposition ...
  • QSAR, machine learning
  • Protein-Protein Docking
A registration form can be downloaded here.

2009 ICM User Group Meeting: Challenges in Protein Structure Prediction and Drug Design

Please join us at our ICM User Group Meeting on April 9th and 10th to be held in La Jolla, CA. Come and hear about the latest developments in: Structure and Ligand Based Drug Design, Membrane Protein Modeling, Protein Structure Analysis, Virtual Ligand Screening, Protein-Protein Docking, Data Visualization, and Chemical Biology. The registration fee for Academics is $99 and for Commercial is $300. A registration form can be downloaded here.

New ICM Publication : Type-II Kinase Inhibitor Docking, Screening, and Profiling Using Modified Structures of Active Kinase States. Kufareva and Abagyan J. Med Chem

Download the paper here.

Abstract:Type-II kinase inhibitors represent a class of chemicals that trap their target kinases in an inactive, so-called DFG-out state, occupying a hydrophobic pocket adjacent to the ATP binding site. These compounds are often more specific than those that target active DFG-in kinase conformations. Unfortunately, the discovery of novel type-II scaffolds presents a considerable challenge, partially because the lack of compatible kinase structures makes structure-based methods inapplicable. We present a computational protocol for converting multiple available DFG-in structures of various kinases (?70% of mammalian structural kinome) into accurate and specific models of their type-II bound state. The models, described as deletion-of-loop Asp-Phe-Gly-in (DOLPHIN) kinase models, demonstrate exceptional performance in various inhibitor discovery applications, including compound pose prediction, screening, and in silico activity profiling. Given the abundance of the DFG-in structures, the presented approach opens possibilities for kinome-wide discovery of specific molecules targeting inactive kinase states.

Floating Licenses for the Mac

Due to customer demand we now offer floating licenses for the Mac platform. A floating license is placed on a server and any client computer connected to the server can “check out” the license. In the past all ICM licenses for Mac were locked to a particular machine (nodelocked license). The floating license option now gives you more flexibility in your ICM use if you need it. You can receive a floating license for Mac the next time you renew or purchase a new license.

New Features in the Latest ICM Version

The new ICM developments are listed in the Release Notes here. In particular please see:
  • Lots of new developments in the ICM Ligand Editor
  • New selections for Hbond donors and acceptors
  • New table coloring options

ICM Power Tip: Chemical searching very large databases.

ICM tables are capable of storing tens of thousands records. However, some problems operate with data sets so large that they do not fit in computer's memory. To work with such large amounts of data ICM uses the concept of Molsoft database (MOLT) files. Unlike many other table file formats, such as SDF, CSV and others, database files are optimized for fast search and other operations, like unique entry addition and diverse subset selection. To learn how to make a MOLT file and search see here.


November 2008 Newsletter

Welcome to the November 2008 MolSoft ICM Newsletter containing information on:

  • New ICM Cheminformatics Products Released: ICM Chemist and ICM Chemist Pro
  • Join us at the ICM User Group Meeting in April next year
  • 2009 ICM Workshops - Protein Structure and Drug Design Dates
  • Google Search the ICM Manuals
  • See ActiveICM in Action
  • A New 3D File Format
  • ICM Method Publication: Atomic Property Field Superposition
  • Join the ICM Discussion Forum
  • ICM Power Tip: How to Make Molecular Movies in ICM

New ICM Cheminformatics Products Released

We are pleased to announce the release of two new stand alone Cheminformatics products called ICM Chemist and ICM Chemist Pro. ICM Chemist is a low cost feature-rich product for dealing with chemical structure and databases. The ICM Chemist Pro product contains all the features in ICM Chemist and gives you access to the 3D world of chemical viewing and manipuation. Some of the main features of each of the products are listed below

ICM Chemist Features

  • Read in and save chemical structures in a variety of formats.
  • Draw and edit chemical compounds.
  • Chemical Spreadsheets: Rich environment for display, manipulation and analysis of chemical datasets, from a few compounds to ~100K. For more than 100K you can use our MOLT file format (see below) and /or MolCart.
  • Chemical Searching
  • Fast herarchical clustering and trees.
  • Chemical Enumeration, Decomposition by R-Group (Markush Structures).
  • Build Local Databases (MOLT file): Large database files optimized for fast search and other operations such as unique entry addition and diverse subset selection.
  • Apply QSAR models.
  • and much more...
ICM Chemist Pro Features
  • Convert 2D chemical sketches to 3D and optimize.
  • Generate stereoisomers and tautomers.
  • Chemical superposition.
  • 3D interactive ligand editor.
  • QSAR

Join us at the ICM User Group Meeting in April next year

April 9-10 2009 ICM User Group Meeting.

We are looking forward to the 1st ICM User Group Meeting in April next year. The meeting schedule will include talks by experienced ICM users from around the world with an emphasis on how they have successfully used ICM and other applications for their research. MolSoft's developers and scientists will also be presenting at the meeting, so it will offer a good opportunity for you to hear about the latest ICM developments and new features. More information about how to register for the user group meeting and the speakers will be in the next newsletter.

ICM Workshop - Protein Structure and Drug Design Dates

The dates for the 2009 ICM workshops to be held in La Jolla CA are listed below.The workshops will be presented by Prof. Ruben Abagyan (Scripps Research Institute, and Founder of MolSoft ) and Dr. Maxim Totrov (Principal Scientist, Molsoft).

Feb 5-6 2009 - ICM Workshop "Protein Structure and Drug Design"

October 1-2 2009 - ICM Workshop "Protein Structure and Drug Design"

More details here

Google Search the ICM Manuals

The ICM Language Manual and the ICM User Guide Manual can now be google searched. Click here to give it a try. Once you have performed a search you can refine it to only display results from the Language Manual or the User Manual. This search will soon be integrated into the online versions of the manual.

See ActiveICM in Action

Click here to view an example of our new ActiveICM product (US Patent No:7,880,738) in action. The files used in ActiveICM can be generated using ICM Browser Pro, ICM Chemist, or ICM Pro and ActiveICM is free to customers of this product. The online example is a Structural Genomics Consortium datapack file of PAK4 kinase. Use your left mouse button to rotate the molecule, zoom in by clicking on the left hand side of the display, scroll down the text on the left hand side and click on the blue links to see different annotated views of the protein, and right click on the graphical display for more option, and right click on the graphical display for more options.

NOTE: The demo will only work if you download ActiveICM. Click here to download ActiveICM.

New 3D File Format

ICM now supports the 3D XML file format which is a popular 3D format for CAD. For example, Microsoft Virtual Earth uses this file format as well as CAD software companies such as Dassault Systems. There is a big online repository of 3DXML models here, models are free to download once you have registered. Once the file is downloaded, open the ICM graphical user interface, click on File/Open in ICM to bring the file into ICM and then display the file using the ICM Workspace.

New ICM Method Publication: Atomic Property Field Chemical Superposition

The Atomic Property Field (APF) superposition method is available in ICM Chemist Pro and the details of this method have been published this year by Dr. Maxim Totrov (Molsoft, Principal Scientist). Totrov M (2008) Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. Chem Biol Drug Des 71: 15-27 APF is a 3D pharmacophoric potential implemented on a grid. APF can be generated from one or multiple ligands and seven properties are assigned from empiric physico-chemical components (hydrogen bond donors, acceptors, Sp2 hybridization, lipophilicity, size, electropositive/negative and charge). Click here to see how to use the APF method.

Join the ICM Online Discussion Forum

We now have over 80 members in the ICM Discussion Forum but this only represents a very small percentage of the ICM users worldwide. Click here to join the forum today. It is free to join the forum and there are many benefits of being part of this group: you will always be the first to get to know the new ICM features, you will learn new tips and tricks in ICM, find out how others are applying the software in their research, and most importantly you will be part of a network of people who can support and advise you when you have an ICM question. Click here to join the forum today.

ICM Power Tip

Making Molecular Movies in ICM

To make a movie in ICM all you have to do is click on the movie button located at the bottom of the graphical user interface. Any animation or view in the ICM graphical window will then be dumped into a movie file. For more instructions please click here.

07.11.2008 July 2008 MolSoft ICM Newsletter

MolSoft ICM Newsletter July 2008

Welcome to the July 2008 MolSoft ICM Newsletter containing information on:

  • All the exciting new features in ICM version 3.6 and links to the GUI manual.
  • A new product release - ActiveICM allows you to display ICM in PowerPoint and Web Browsers.
  • The next ICM Workshop in La Jolla CA October 2-3, 2008.
  • MolSoft will be at the Protein Society Meeting July 19-23, 2008
  • ICM Power Tip - Quick Ligand/Peptide Pocket Surface Display

New Features in the Latest ICM Release 3.6

Fully Interactive 3D Ligand Editor

The ligand editor is a powerful tool for the interactive design of new lead compounds in 3D. It allows you to make modifications to the ligand and see the affect of the modification on the ligand binding energy and interaction with the receptor. You can eidt the ligand by adding new functional groups, sampling a large collection of fragments on the fly, edit atoms or bonds, and and then in seconds see the affect of these changes on ligand binding. Clashes with the receptor are clearly flagged and energy contributions of each atom and total bidning energy and binding score are provided. Please see the graphical user interface manual for more information and instructions http://www.molsoft.com/gui/ligand-editor.html

Docking a Markush Library

Generate a Markush library and dock a focused version of it on the fly. See this example, optimizing the roscovitine ligand bound to CDK5 http://www.molsoft.com/gui/markush-docking.html

Export Chemical Spreadsheets to Excel

Export the 2D chemical sketch as well as other column data in a spreadsheet directly to Microsoft Excel. See: http://www.molsoft.com/gui/export-excel.html

Read and Display Google Sketchup 3D Images

You can now read, render and display any 3D object in ICM. e.g. KMZ and COLLADA format directly from the google sketchup website. We have also added options for changing the texture and material of a 3D object. See http://www.molsoft.com/gui/google-objects.html

Lots of New Data Plotting Features From ICM Tables

New plotting features include:

  • logarithmic scale
  • separate zooming for X and Y axis
  • zooming into/out of a certain point on the plot
  • Axis customization: setting titles and steps
  • Point labels in scatter plots, showing labels for selection only
  • Interactive control over histogram bin size to allow finding the best density estimation picture

See http://www.molsoft.com/gui/table-plot.html for instructions

Background Images

Add any image you want to the background. This is great for making cool images or you can directly compare molecules by making a background image and then making changes to the molecule and see clearly the differences. See http://www.molsoft.com/gui/background.html

IUPAC Nomenclature

ICM will now determine the IUPAC nomenclature for any small molecule you sketch or read into ICM. See http://www.molsoft.com/gui/iupac.html

Ribbons and Chain Breaks

Display smooth ribbons and control the display of chain breaks See: http://www.molsoft.com/gui/structure-representation.html#ribbon

Local Chemical Databases

In many cases a compound database (sdf file) is so large that you cannot open it in ICM because you do not have enough memory on your computer. A way around this was to place the database on our product called MolCart but now you can build local chemical databases which you can browse and edit.

Some of the features include:

  • Import SDF, CSV/TSV, ICM tables
  • Search (chemical)
  • Manage databases: rename/delete tables.
  • Clustering (selecting a representative set)
  • Editing (deleting/inserting/modifying)
  • Export SDF, CSV/TSV

For more information please click here http://www.molsoft.com/gui/local-databases.html

Occlusion Shading

The occulusion shading option provides better representation of depth within a cavity. The color of each surface element of a grob (mesh) is changed by mixing its own color with the background depending on the burial of the surface element. See http://www.molsoft.com/gui/mesh-options.html#occlusion-shading

Protect Objects From Deletion

This option is useful when making molecular documents and you do not want the viewer of the document to delete an object that is contained in the document. See: http://www.molsoft.com/gui/make-molecular-document.html#protect

Wide-Screen Layout

There is now a new layout for users that have a widescreen. Try it by going to File/Preferences/Gui Tab and change GUI.windowLayout

New Command Line Options

Other new command line options are described in the release notes .

New Product - ActiveICM

ActiveICM - Integrate ICM into PowerPoint or a Web Browser

ActiveICM will change the way you give presentations or share ICM data with your colleagues. With ActiveICM you can display a series of slides generated in ICM inside PowerPoint or a web browser. The slides are fully interactive which means the user can manipulate the molecules in 3D inside the viewer. Click here to wownload ActiveICM and see the instructions here http://www.molsoft.com/gui/activeicm.html

Next ICM Workshop

The next ICM workshop will be held in La Jolla CA on October 2nd to 3rd. The workshop will be presented by Prof. Ruben Abagyan (Scripps Research Institute, and Founder of MolSoft ) and Dr. Maxim Totrov (Principal Scientist, Molsoft). See http://www.molsoft.com/training.html

Events - 2008 Protein Society Meeting

If you are attending the Protein Society 22nd Annual Symposium July 19-23, 2008 in San Diego be sure to stop by the MolSoft booth and say hello. We will be holding prize draws, demonstrating all the new ICM features, and we will be available to answer any ICM questions you may have.

ICM Power Tip

Quick Ligand and Peptide Pocket Display

Did you know you can quickly display the surface of a ligand or peptide by pocket by right clicking on the ligand or peptide in the ICM workspace and selecting Ligand Pocket. See http://www.molsoft.com/gui/dsPocket.html


06.20.2008 MolSoft @ Bio 2008

There were over 20,000 people at the Bio 2008 meeting and we thoroughly enjoyed demonstrating the latest ICM features and answering questions from the many people who stopped by at our booth. It was great to see so many ICM-users at the meeting and meet for the first time some of our international customers from Europe, Australia, and Japan. We received great feedback on our new ligand editor feature which will be released very soon, and our molecular document technology also attracted alot of interest. Other pictures from Bio2008 can be found here.

05.22.2008 MolSoft will be Exhibiting at Bio2008

MolSoft LLC is looking forward to presenting at the Bio2008 conference in San Diego June 17-20. Please come and visit us at booth #2539 where we will be showcasing for the first time lots of exciting new tools that will be released later this year in ICM Version 3.5-2.

04.08.08 New ICM Paper: New method for the assessment of all drug-like pockets across a structural genome.

Nicola G, Smith CA, Abagyan R. New method for the assessment of all drug-like pockets across a structural genome. Comput Biol. 2008 Apr; 15(3):231-40.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California.

Abstract: With the increasing wealth of structural information available for human pathogens, it is now becoming possible to leverage that information to aid in rational selection of targets for inhibitor discovery. We present a methodology for assessing the drugability of all small-molecule binding pockets in a pathogen. Our approach incorporates accurate pocket identification, sequence conservation with a similar organism, sequence conservation with the host, and structure resolution. This novel method is applied to 21 structures from the malarial parasite Plasmodium falciparum. Based on our survey of the structural genome, we selected enoyl-acyl carrier protein reductase (ENR) as a promising candidate for virtual screening based inhibitor discovery.

03.20.08 New ICM Publication: A new method for ligand docking to flexible receptors

New ICM publication by the Scripps Research Institute and MolSoft scientists. See: Bottegoni G, Kufareva I, Totrov M, Abagyan R. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des. 2008 Feb 14;

Paper link:

Abstract Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded a previously used diverse "cross-docking" benchmark to thirty ligand-protein pairs extracted from different crystal structures. The algorithm systematically scans pairs of neighbouring side chains, replaces them by alanines, and docks the ligand to each 'gapped' version of the pocket. All docked positions are scored, refined with original side chains and flexible backbone and re-scored. In the optimal version of the protocol pairs of residues were replaced by alanines and only one best scoring conformation was selected from each 'gapped' pocket for refinement. The optimal SCARE (SCan Alanines and REfine) protocol identifies a near native conformation (under 2 A RMSD) as the lowest rank for 80% of pairs if the docking bounding box is defined by the predicted pocket envelope, and for as many as 90% of the pairs if the bounding box is derived from the known answer with approximately 5 A margin as used in most previous publications. The presented fully automated algorithm takes about 2 h per pose of a single processor time, requires only one pocket structure and no prior knowledge about the binding site location. Furthermore, the results for conformationally conserved pockets do not deteriorate due to substantial increase of the pocket variability.

03.11.08 Free Online Tutorial Dates Released for May through to July.

Click here for information on the upcoming online demonstrations.

03.03.08 New Review Article from MolSoft on Flexible Docking

Here is a link to a new publication in Current Opinion Structural Biology on flexible docking by Dr. Totrov (MolSoft) and Prof. Abagyan (Scripps). The paper highlights all the recent development for including multiple receptor conformations in docking to represent ligand induced fit.

02.14.08 New Tutorial: How to model the effect of a mutation on protein structure.

Click here for a new tutorial on how to make a mutation in a protein structure and optimize.

02.14.08 MolSoft Scientists Collaborate with Schering Plough to Identify New GPCR Inhibitors using ICM.

Click here to read how MolSoft and Schering Plough scientists identified new inhibtitors for a GPCR using MolSoft's drug discovery products. The structure-based development of MCH-R1 and other GPCR antagonists is hampered by the lack of an available experimentally determined atomic structure. A ligand-steered homology modeling approach has been developed (where information about existing ligands is used explicitly to shape and optimize the binding site) followed by docking-based virtual screening. Top scoring compounds identified virtually were tested experimentally in an MCH-R1 competitive binding assay, and six novel chemotypes as low micromolar affinity antagonist "hits" were identified. This success rate is more than a 10-fold improvement over random high-throughput screening, which supports our ligand-steered method. Clearly, the ligand-steered homology modeling method reduces the uncertainty of structure modeling for difficult targets like GPCRs.

02.04.08 New Tutorial: How to dock to multiple receptor conformations.

There is a new tutorial online here

The tutorial uses Aldose Reductase as an example. Aldose Reductase has a flexible loop in the ligand binding pocket vicinity which enables a variety of inhibitors to bind and therefore in order to identify these ligands via docking it is necessary to sample the conformations of this loop and dock to an ensemble of structures.

2007

12.15.07 New Docking tutorials - Docking to Electron Density and Focused Markush Library Docking

How to dock a ligand to an electron density map. The ICM X-Ray AutoFit is an automated method to fit a ligand into electron density. The tool combines the powerful ICM docking algorithm with an electron density fitting function. Click here for step by step instructions.

How to dock a focused Markush library. A Markush library can be generated on the fly and docked using ICM. In this example we use the roscovitine ligand bound to CDK5 to identify scaffolds which may improve ligand-receptor interaction.

10.23.08 New Slide Transition EffectIn ICM version 3.5-1l a new blending transition effect between slides is available. To see this in action download the latest version of ICM or the free ICM-Browser and view this icb file:

http://www.molsoft.com/~andy/blend.icb

To generate this transition effect:

  1. Make a couple of slides - click camera button at bottom of the gui - Note: to see the blending transition the transition needs to be made between different representations eg wire to ribbon
  2. Right click on the name of the slide in the ICM workspace and select edit slide
  3. At the bottom of this window you will see options for the currently available transitions - blend and smooth - check which one you would like to use and the transition time in ms.

October 22nd 2007

As a quarter of million people fled their homes amid fierce wildfires that had burned 100,000 acres around San Diego County, Molsoft opened its doors for the families of the escapees. Children, pets, and adults have found a comfortable home at Molsoft and were given a place to stay, sleep, access internet and play video games.

Games, food, laughter and partial property destruction made their stay at Molsoft more comfortable. The training class became an information center from which the families were following the fate of their homes.

October 17th 2007

MolSoft launches the ICM Forum. Please sign up and contribute with questions/answers and interact with other ICM users worldwide.

October 12th 2007

MolSoft announces a series of online demonstrations as a new way of teaching the ICM suite of software. Click here for more information.

July 12th 2007

Molecular Movie Making Made Easy
Real-time screen grabbing movie making is now available in ICMBrowserPro on all platforms. With one click of the mouse anything displayed in the graphical displaywindow will be transfered to movie format - mpeg, avi or mov. See an example of an ICM movie here.

June 2nd 2007

MolCart Compound Database Update
The MolCart Compound screening library has been updated. The database contains 3,621,728 unique compounds for use in MolCart. Please contact info@molsoft.com for more information on licensing MolCart.

May 25th 2007

The latest version 3.5 for all ICM products has been released for Windows, Mac , Linux and SGI.Please download the latest version of ICM from our support center.

Some of the new features include:

  • Screen-grabbing movie making - one click movies saved in mpeg, avi or mov format.
  • Multiple-receptor docking to represent flexibility within the ligand binding site.
  • Faster machine learning tools for QSAR.
  • Over 20 new chemistry menu options added.
  • Improved graphics and new styles for xstick, variables, transparent CPK, hydrogen bonding, chain gaps.
  • New data plotting tools.

For more details please see the Release Notes.

March 27th 2007 Maxim Totrov PhD to present data at American Chemical Society National Meeting

On March 27th 2007 Dr. Maxim Totrov (Principal Scientist - MolSoft LLC) will be giving a presentation entitled "Chemical superposition and pharmacophore elucidation by SCAPFOld: Self-consistent atomic property field optimization" at the American Chemical Society 233rd National Meeting & Exposition, Chicago, IL USA. The presentation abstract can be found here.

March 22nd to 23rd 2007 ICM Workshop

Once again the ICM Workshop sold out quickly and we had a full class of students eager to learn about Protein Structure and Drug Discovery using MolSoft's ICM software. The first day and a half of training was presented by Prof. Ruben Abagyan (Scripps Research Institute). Prof. Abagyan gave lectures and demonstrations on ICM sequence and structure analysis, molecular modeling and cheminformatics. Friday afternoon was devoted to small molecule docking, virtual ligand screening and protein-protein docking led by Dr. Maxim Totrov (Principal Scientist - MolSoft). The participants ran docking examples such as virtual screening of small ligand databases to identify known inhibitors of the cyclooxygenase receptor and protein-protein docking of subtilisin and chymotrypsin. All the participants agreed that the workshop will help them greatly when they return to the lab and would highly recommend the training to their colleagues.

If you were unable to attend this workshop we are holding workshops in May and September this year. Please click here for more details and sign up early to guarantee your place.

2006

August 1st 2006 MolSoft Awarded NIH SBIR Phase I Grant to develop protein surface annotation software

MolSoft was recently awarded a NIH SBIR Phase I Grant to develop an integrated protein surface annotation suite of software for biologists and chemists. The software will allow users to apply several binding site prediction methods and analyze the results. These new algorithms include a protein-protein interface prediction method for small molecule binding sites and a surface structural motif detection and visualization method.


July 1st 2006 MolSoft Receives Bill and Melinda Gates Foundation AIDS Research Grant

Scientists at MolSoft LLC will be working as part of a multidisciplinary team led by Susan Zolla-Pazner Ph.D. (New York University School of Medicine) on a grant funded by the Bill and Melinda Gates Foundation entitled "The V3 Loop: A Conserved Structure of gp120 that Can Induce Broadly Neutralizing Antibodies Against HIV-1"

MolSoft LLC is excited to be leading the structure-based engineering of the V3-carrier immunogen. Using our experience with similar efforts we will undertake ab initio loop modeling of protein segments consisting of the central portions of the V3 signature sequences and modeling of carrier joining sequences. For more information please see the press release in the New York Times.


July 1st 2006 MolSoft and Virginia Tech collaborate to work on malaria vector control

MolSoft and Virginia Tech will be working together on a 3-year project funded by the Foundation of the National Institutes of Healt to apply state-of-the-art computer modeling and chemical synthetic approaches to produce highly potent and selective anticholinesterases (AChEs) for malaria vector control. MolSoft's ICM software will be used to build homology models of AChEs and virtual screening will be applied to identify selective inhibitors. ICM-Chemistry will then be applied to optimize the lead compounds.


February 8th 2006: From Physics to Biology: the interface between experiment and computation BIFI 2006 - II International Conference, Zaragoza Spain.

Claudio Cavasotto PhD (Senior Scientist - Molsoft) has been invited to present a talk entitled "Ligand docking and virtual screening in structure-based drug discovery" at the BIFI 2006 - II International Conference, Zaragoza, Spain. His talk will be on February 8th 2006 and more details about the conference can be found here.


January 25th-27th 2006 Three-Day ICM Workshop.

On January 25th-27th 2006, a 3-day ICM Workshop was held at Molsoft's La Jolla offices. The first two days of the workshop covered all aspects of protein structure and drug discovery including sequence analysis, protein modeling, small molecule docking, protein-protein docking, cheminformatics and QSAR. The third day was dedicated to advanced ICM training including the ICM command language, scripting, loop modeling and flexible receptor docking. The course was conducted by Prof. Ruben Abagyan (The Scripps Research Institute) and Dr. Maxim Totrov (Principal Scientist - Molsoft).



January 1st 2006 MolSoft and the Mayo Clinic College of Medicine Collaboration

Scientist at the Mayo Clinic and MolSoft will be collaborating on a project to model G-protein coupled receptors (GPCRs) which are key receptors for a large number of disease pathways. The aim is to use MolSoft's proprietary software to build highly-refined and rigorously validated models of GPCRs and to use these models to guide experimental work at the Mayo Clinic.


2005

September 29th-30th 2005 Successful Workshop

On September 29th-30th an international group of ICM users from academia and industry gathered for our ICM Workshop entitled "Protein Structure and Drug Discovery" Click here to see what went on.


August 3rd, 2005 New Version Release

Molsoft has released the latest version (3.4) of ICM. This version includes a number of new features as described in the Release Notes. The most significant addition is the incorporation of ICM Molecular Documents and Presentation (US Patent No:7,880,738). These can be constructed and viewed in ICM, they can consist of text linked to molecular animations and transitions. The animations and transitions are fully-interactive and can be interrupted without any loss of information. For more information on ICM Molecular Documents and Presenations please click here.


April 14th, 2005 New Product Release.
MolCart is the latest addition to the ICM suite of software. MolCart allows you to store and manipulate large chemical databases which can then be searched and analyzed using ICM cheminformatics tools.


April 25th, 2005 New SGI version release.
A new ICM SGI version - 3.3-04c has been released. Please click here to download the latest version.


April 5th, 2005
The Latest version of ICM (3.3-04) has been released. Please click here to download the latest version. Release Notes.

2004

August 10th, 2004
Press Release:San Diego, CA. Molsoft LLC and the Structural Genomics Consortium at the University of Oxford Announce Software Co-Development and Research Collaboration. more details


July 15th, 2004
Molsoft LLC is pleased to announce a collaboration with the Burnham Institute, La Jolla, on a Tobacco-Related Disease Research Program Funded Grant entitled "Vitamin A Derivatives as Antagonists of Nicotine Effects".


July 30, 2004 California State University at Fullerton Expands Use of ICM-Pro to New Computational Biology Curriculum Being Offered in 2005-06

Molsoft is pleased to learn that the Department of Chemistry and Biochemistry at California State University, Fullerton, is expanding its teaching use of ICM-Pro. CSU Fullerton began using ICM-Pro for training undergraduate chemistry and biochemistry students in Spring 2004. ICM-Pro has also been used to teach structural bioinformatics to students seeking a Certificate in Bioinformatics through CSUFs Extended Education program. Beginning in 2005-06, ICM-Pro will be featured in a new computational biology program for chemistry and biochemistry majors [more].


July 20-21st Molsoft Conducts ICM Workshop in New Jersey USA

On the 20-21st of July 2004 sixteen people attended the ICM workshop entitled "In Silico Drug Discovery". The workshop was held at Bristol Myers Squibb at Princeton New Jersey.


June 25th, 2004

Molsoft LLC is pleased to announce a collaboration with the Burnham Institute, La Jolla, on a STTR NIH funded grant entitled "15 - Deoxy -12,14-prostaglandin J2 as a ligand of RXRalpha".


March 17, 2004 Molsoft LLC Receives Phase I STTR to Develop Beta-Catenin Antagonists

Molsoft LLC received a Phase I STTR award from the National Institutes of Health, National Cancer Institute, for the project entitled. Rational Development of TCF/Beta-Catenin Antagonists. The project will combine Molsoft's novel in silico lead development platform with the cancer biology resources at The Burnham Institute to discover and characterize small molecule ligands using the beta-catenin structure both alone and in complex with TCF. Beta-catenin signaling has been implicated in a number of malignancies, which makes the beta-catenin/TCF interaction an promising target for the prevention and treatment of a variety of tumors and leukemia, and the project proposes to develop a novel generation of drugs active against various forms of cancer.


2003

July 25, 2003 Molsoft LLC Receives Small Business Biodefense Grant Award

Molsoft LLC received a Small Business Biodefense Program award from the National Institutes of Health, National Institute of Allergy and Infectious Diseases, for the project entitled .Rational Design of Inhibitors of Yersinia pestis EF-Tu.. Molsoft and its research partners at the University of California, Irvine and Chemical Diversity Labs, Inc., San Diego, propose to develop a new class of antibacterial agents active against Category A pathogens likely to be used by bioterrorists including those causing plague, anthrax, cholera, and typhoid fever. Furthermore, the project proposes to develop design principles that will be useful in developing agents less susceptible to the problem of rapidly emerging antibiotic drug resistance.


18 June 2003.Mpex Pharmaceuticals and Molsoft announce collaboration for the structure-based design of new antibacterial compounds.

Mpex Pharmaceuticals Inc. (“Mpex”) and Molsoft, LLC (“Molsoft’) have announced a collaboration to rationally design new antibacterial agents based on the refinement of a 3-D molecular structure of a membrane protein target, the functional characterization of its surfaces, and the application of predictive algorithms ..more..


June 16, 2003 Molsoft LLC Receives Phase II STTR Grant Award to Continue Developing Thyroid Receptor Antagonists

Molsoft LLC received a Phase II STTR award from the National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, for continuation of the "Rational Development of Thyroid Receptor Antagonists. project. In Phase I, Molsoft and its collaborators at the NYU School of Medicine and the NYU Department of Chemistry achieved proof of concept. Molsoft.s virtual ligand screening technology was used to discover 14 small molecule thyroid receptor antagonists displaying extreme structural diversity with IC50s ranging from 4 to 30 microM. Additionally, the test-case lead optimization scheme designed in Phase I based on generating focused virtual libraries of molecules easily amenable to organic parallel synthesis resulted in the rapid identification of second generation hits with IC50 in the nanomolar range. In Phase II, Molsoft and its NYU research partners propose to conduct full-scale optimization cycles of selected hits identified in Phase 1 in order to produce low nanomolar hits and to evaluate those hits using computational tools, in vitro characterization, and preliminary animal studies.


May 20th-21st 2003 Molsoft LLC Conducts Annual Spring Training CourseOn the 20-21st May 2003 conducted an ICM workshop entitled "In Silico Drug Discovery". The workshop was held at Molsoft LLC La Jolla.

2002

21 October 2002. Molsoft to Evaluate Novel Scaffolds for PDF Inhibitor Program

Molsoft LLC, a La Jolla based company providing new, breakthrough technologies in computational chemistry and biology, and GeneSoft Pharmaceuticals Inc., a specialty pharmaceutical company headquartered in South San Francisco, announced that they have signed a collaborative agreement to evaluate inhibitors of peptide deformylase (PDF), an essential bacterial metalloenzyme and novel antibiotic target ..more...


26 August 2002. Molsoft Conducts Training Course/ Workshop in La Jolla, CA

Molsoft conducted an intensive 2-day training course/workshop on the ICM suite of products at La Jolla, CA. The lecture and hands-on demonstrations covered topics of interest to computational chemists and biologists in the area of drug discovery. The topics included molecular graphics, animation, bioinformatics, homology, protein modeling, docking and ICM command language for expert users.

The attendance was international with scientists coming from Asia and Europe as well as from various parts of the US. The attendees were interested in having future courses, both at the basic and at the advanced levels.

One of the attendees from Australia who is very well known in the modeling field for his early work in structural bioinformatics, Dr. Jiri Novotny (Consultant for Biocomputing and Bioinformatics), said, "The course was well organized and presented the participants with two full days of new and efficient tools applicable to the most pressing problems of current structural biology and bioinformatics: structural/functional annotation of genomic data, analysis of protein surfaces, ligand binding sites, virtual ligand screening, structure derivation, regularization and model building". He continued on to say, "Perhaps the most impressive aspect of the workshop was the skill, dedication and the highest professional standard of the scientific team established at Molsoft by Prof. Abagyan. In hands-on session at computer screens the participants were encouraged to ask questions and bring out problems that were answered and solved immediately by the whole team including themselves. It was an invaluable practice and a good demonstration of the speed and versatility of the newest ICM version."

The new version, ICM 3.0, was introduced at the course and was well accepted as an extremely user-friendly interface by the attendees. This version, which also has stereo viewing mode that works with VRex glasses on Linux and Windows platforms, was welcomed by all the participants as an efficient and low cost alternative to existing stereo viewing tools.

About the training course, Dr. Maxim Totrov, co-founder and Principal Scientist at Molsoft said, "The course provided us with a vital opportunity to meet members of the growing community of ICM-users and bring them up-to date with the latest developments in ICM. It was exciting to see first-time users perform complex molecular modeling tasks such as protein-ligand docking after only a few hours of training. These workshops are geared towards helping our customers utilize fully the power of ICM molecular modeling suite in their everyday work."


22 August 2002. Molsoft Participates in the Annual Symposium of the Protein Society in San Diego

Molsoft is pleased to announce its participation at the Protein Society's 16th Annual Symposium held at the Marriott in San Diego from August 17-21, 2002. Attendance was estimated at around 1300. Molsoft's exhibit was designed to inform Protein Society attendees about the latest technology available from Molsoft including its recent version of a new graphical interface which enables Molsoft's ICM software easier to use than ever before.

"We enjoyed talking to numerous visitors to our booth," said Dr. Lalitha Subramanian, Director of Contract Research for Molsoft, "many of whom were extremely excited to see ICM's new GUI interface." She added, "Our science has always been strong and well validated. Now, with the added power of a very user friendly interface, ICM will be the choice for most researchers in the academic and commercial fields."

Molsoft also participated in the Beyond Genome 2002 conference held in June of this year and will be presenting at the BioITWorld conference to be held in November.


Molsoft LLC Receives Phase II SBIR Grant Award May 21, 2002

Molsoft received a Phase II SBIR award from the Department of Energy for continuation of the "GAP: Genomics Annotation Platform" project. In Phase I Molsoft used its many years of experience in developing molecular visualization and manipulation software to built the computational tools central to the functionality of the GAP. In Phase I, Molsoft successfully used GAP to predict the function of uncharacterized genes. In Phase II, Molsoft will optimize the existing tools and develop an efficient graphical user interface while adding a system for automatic updates to GAP. When completed, the Molsoft GAP will provide an online research platform allowing users from the pharmaceutical industry to access Molsoft's state-of-the-art computational biology technology and to use that technology for extracting meaningful information from the human genome project and from other major, international sequencing efforts.


March 2002

Molsoft received a Phase 1 SBIR grant from the National Institutes of Health, National Human Genome Research Institute for its project entitled "Sequence/Structure Annotation of Protein Families." The goal in this project is analyzing in silico well known protein families in order to identify which family members could be good therapeutic targets and how pharmacogenomics strategies can be devised to better design drugs targets at these proteins.

2001

August 2001

Molsoft and Plexus Vaccine Inc.entered into a licensing agreement to discover and commercialize new interventional strategies for global infectious diseases, for drug-resistant microbes, and for chronic diseases associated with cryptic pathogens. Plexus will use the Molsoft ICM software suite to develop Virtual Epitope databases of molecular disease targets for in silico design of structural mimics that can be readily synthesized, tested, and formulated as vaccines ..more..


August 2001

Molsoft received a Phase 1 SBIR grant from the Department of Energy for its project entitled "GAP: Genomics Annotation Platform." The goal in this project is to develop bioinformatics tools used for predicting the function of uncharacterized genes.


May 2001

Molsoft and HTS Biosystems, Inc. (HTS) entered into collaboration for Molsoft to develop software modules for instrument control, data collection, local visualization, and analysis of data generated by HTS' Surface Plasmon Resonance (SPR) instruments.


April 2001

Molsoft LLC and Chemical Diversity Labs, Inc. (CDL), San Diego, CA, formed a strategic alliance to provide joint chemistry and computational modeling services to their customers. Molsoft will use known three-dimensional structures of drug targets as the starting point for the rational selection process. The Molsoft modeling by homology technology will be applied in cases when the structure is not available. CDL will give Molsoft an access to its collection of over 250,000 diverse purified small molecules already available for biological screening.


February 2001

Molsoft and Biovitrum AB, a subsidiary of Pharmacia & Upjohn AB, entered into an agreement to co-develop a Chem-Informatics Client System. Molsoft and Biovitrum will use Molsoft's proprietary programming languages and libraries to develop the software, which will be called BeeHive and will function as a program manager and database interface for chemical searches, analysis, and integration.

2000

November 2000

Molsoft has moved to a new location, click the press release for more details.

October 2000

Molsoft and Syrrx, Inc., a pioneer in the field of structural proteomics, entered into a strategic alliance to accelerate structure-guided drug discovery through the combination of Molsoft's Virtual Ligand Screening (VLS) technology and other computational biology technologies with Syrrx's high-throughput structural proteomics platform. ..more..

September 2000

Molsoft received a Phase 1 STTR grant from National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases for its project entitled "Rational Development of Thyroid Receptor Antagonists." The goal of this project is to discover and optimize small molecule antagonists of the thyroid hormone receptor. Molsoft will work with the New York University School of Medicine to complete the project.

September 2000

Molsoft LLC announced the relocation of its headquarters and commercial development operations to an expanded facility in La Jolla. The new facility will accommodate several expanded programs, including the continued refinement of ICM 2.8, the expansion of software sales and the addition of new products and in-house services. The new facilities include 3500 square feet of computer laboratory, research, training, and office space in close proximity to The Scripps Research Institute and the Genomics Institute of the Novartis Research Foundation (GNF), both of whom have research collaboration agreements with Molsoft.

September 2000

Molsoft LLC announced its first shipment of the Molsoft BioPackage to Hitachi, Ltd. for distribution in Japan. During the two-year Distribution Agreement, which became effective June 1, 2000, Hitachi will be the exclusive distributor of Molsoft's BioPackage in Japan. Hitachi plans to market the software to Japanese corporations, universities, and laboratories. Molsoft's computer software provides novel computational and informational technologies for biomedicine including genomics and drug discovery. ..more..

April 2000

Molsoft and The Genomics Institute of the Novartis Research Foundation (GNF) have entered into a Research Collaboration Agreement. The collaboration will focus on the further development of computational biology tools for functional and structural annotation of new genomic sequences, protein modeling, and virtual ligand screening. Molsoft will provide its ICM software for research in functional and structural annotation of new genomic sequences, protein modeling and lead discovery at GNF, which will provide GNF researchers with an accurate, speedy and flexible method for structural annotation and protein structure modeling. Molsoft will grant GNF a nonexclusive license to use Molsoft databases and software in gene discovery, functional genomics, and drug discovery, and GNF will supply support for personnel and computer facilities to be used in the joint tool development projects ..more..

July 2000

Molsoft LLC and The Scripps Research Institute (TSRI), a private, non-profit research organization engaged in basic biomedical research, announced the formation of research collaboration. During the term of the agreement, TSRI and Molsoft will collaborate on defined joint projects involving the functional and structural annotation of new genomic sequences and protein modeling. For the joint projects, Molsoft will grant TSRI a nonexclusive and restricted license to use Molsoft databases and software in gene discovery, functional genomics and drug discovery, and TSRI will supply personnel and computer facilities for use in the joint projects. ..more..

1999

November 1999

Molsoft LLC and eBioinformatics, Inc. announced the formation of an alliance in which Molsoft will provide its ICM software for incorporation into eBioinformatics, Inc. flagship product BioNavigator. The Molsoft-ICM suite of computational biology tools will provide BioNavigator users with access to the latest and most powerful algorithms. This alliance will give scientists new opportunities based on the power of Molsoft's ICM software and the convenience of BioNavigator's web-based bioinformatics workspace ..more..

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