New Features

• Plot Concentration vs pH
• Plot Charge vs pH
• List Species at pH

• New GIGA sized libraries for screening with RIDE are available including: NIH-SAVI, Enamine REAL, WUXI Galaxi. Download links to the new RIDE formatted databases are here.
• RIDE now supports screening of multiple databases in one run from the GUI or Command line.
• Introduced compressed new RIDE database format which uses ~4-6 times less disk space and faster reading.

• extended .se polypeptide sequence format with unnatural amino acid modifications e.g. trp{hz3_F} is 5-fluoro tryptophane. Format also supports modeling of residue-residue cross-link 'staples'.
• secondary structure bias or restraints, for example one can keep a peptide alpha-helical during docking.

A guide to the coloring and representation of the 2D display:

• Green shading represents hydrophobic region.
• Blue shading represents hydrogen bond acceptor.
• White dashed arrows represents hydrogen bonds.
• Grey parabolas represents accessible surface for large areas.
• Broken thick line around ligand shape indicates accessible surface.
• Size of residue ellipse represents the strength of the contact.
• 2D distance between residue label and ligand represents proximity.
• Covalently bound residue represented with thick black line around ellipse.

• Modification history table: Every ligand modification is stored and recorded in a chemical spreadsheet. Double click on the spreadsheet to view the change. [Documentation]
• Hetero atom scan around ligand: This option allows you to scan groups and hetero atoms at multiple locations on the ligand. [Documentation]
• R-group scan around ligand: This option allows you to scan groups and hetero atoms at multiple locations on the ligand. [Documentation]
• One click 2D interaction diagram: This option creates a 2D interaction map between the ligand and receptor. [Documentation]
• Simple way to analyze ligand-receptor contacts. [Documentation]

• Support for MMTF format. The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structural data quickly and accurately. MMTF is now supported in the latest ICM version it does not have any limitation on number of atoms and is easier to use than the original PDB. The image on the left shows the entire HIV-1 capsid (~2.4 million atoms PDB:3j3q).
• Retina support on Mac.
• Support for GROMACS trajectory files (Tools/Play Trajectory).
• Support for multi graphics windows. [Documentation]
• Quick ligand pocket interaction visualization. [Documentation]
• There is now an option for building a heatmap from data contained within a table. [Documentation]
• There is now an option to add annotations to a plot. [Documentation]

Cheminformatics

Convert Prodrugs to Drugs and Drugs to Prodrugs using a set of reactions [Documentation] Flip boat to chair conformation in the Ligand Editor (Choose Advanced Button and select Apply Templates). Other templates will be added soon. Calculate Maximum Common Substructure [Documentation] R Group Decomposition from Clustering Node [Documentation] Improved pKa auto charge models. [Documentation] Auto close tree mode to make cluster trees more compact. [Documentation]

Docking and Screening

• Add docking restraints by selecting atoms in the receptor. An interacting moiety in the ligand can also be defined. [Documentation]

Protein Modeling and Design

Scan residue pairs for the prediction of disulfide bonds. [Documentation] Multi-template modeling. [Documentation] Torsion Angle Scanning [Documentation] Search the PDB for similar loop conformation. [Documentation] Calculate relative residue frequency in similar loops from the PDB [Documentation] New to the GUI - Sample Peptide using Biased Probability Monte Carlo [Documentation] New to the GUI - Sample Protein [Documentation] Generate low energy water molecule configurations [Documentation]

Bioinformatics

Create a sequence alignment profile and plot it onto an alignment. [Documentation] Sequence Editor Display and edit sites on a sequence. [Documentation]

Version 3.8-4

MolScreen

• New Docking to Protein Pocket Classification/Regression models (dpc) [Documentation]
• Build a custom model panel [Documentation]
• Make a classification model based on your own data or directly from ChEMBL [Documentation]
• Make a APF Docking SAR model based on your own data or directly from ChEMBL [Documentation]

Docking and Screening

A method to calculate the ligand interaction fingerprint from a hitlist has been developed. The fingerprint is a bit string representing a contact with each atom. For specificity there is a special subset of bit strings which represent hydrogen bonding. [Documentation]

Cheminformatics

• Direct link to the ChEMBL databases allows you to search and output chemical and activity data to a chemical spreadsheet [Documentation].
• Direct link to the SureChEMBL chemical patent database [Documentation].
• Free radicals are now supported in 2D and 3D. [Documentation]
• Enumerate formal charge states. [Documentation]

3D Ligand Editor

• Explicit side-chain support has now been added. [Documentation]
• Minimize the ligand in full atom model inside the receptor as well as in the grid maps. [Documentation]
• An option to keep "tight waters" on receptor setup has been added. [Documentation]
• A more interactive way to impose tethers and distance restraints. Each restraint is placed in a table and the values of the restraint can be edited. [Documentation]
• A convenient way to close and clean up your ligand editor session. [Documentation]

Predicting the Effect of Mutation Two new options:

• Predict the effect of mutation on Protein-Peptide. [Documentation]
• Predict the effect of mutation on Proein-Ligand. [Documentation]

New modeling options have been added and old ones improved. The modeling options are:

• Quick Model This option will provide a model by placement of the aligned polypeptide chain onto the template structure. The method is fast and is ideal if you want a quick model for visualization purposes. [Documentation]
• Full Model Builder This option will give you a fully refined model and can take many hours to complete the model building process. There are options to fully refine side-chains, refine side-chains and loops or undertake a full refinement. The refinement is undertaken using the ICM BPMC modeling method in the ICM force field which includes surface terms, electrostatics with the boundary element solution of the Poisson equation and side chain entropy terms. [Documentation]
• Multi-Template Model Editor. This option is ideal if you want more control over your model - particularly in loop regions or if you want to use multiple templates. It provides an interface to add new templates to a model and browse through multiple conformations of loop regions. It also provides an interactive visualization interface to see how well the residues in your model falls into the Ramachandran Plot and how good the omega angles are. [Documentation]

Learn and Predict

• Bayesian and Random Forest methods added to GUI. [Documentation]

Protein-Protein Docking

Fast Fourier Transform (FFT) docking method has been developed. The docking method contains two stages:

1. The first stage uses a simplified scoring function representing steric fit and hydrophobic/hydrophilic contact matching. FFT is then used for translational search using systematic search of rotations from 60x27 (coarse) to 256x125 (fine) orientations.
2. The second stage rescores the top 3000-20000 solutions with a more accurate energy function including electrostatics and SAS-based solvation. The conformations are then clustered using contact fingerprints.

December 20th 2014: Version 3.8-3 Released

3D Ligand Editor

• The 2D editor can now be embedded in the ligedit tab panel (see image). Any changes in the 2D editor can be committed to 3D with a single click. Documentation
• Any change in 3D can be automatically saved to a spreadsheet but now if you click and hold on the button you can add a tag or comment to the saved chemical in the spreadsheet. Documentation

KNIME

• New MolCluster node is available - you can cluster either by fingerprints or by numerical column selection. The output will contain two additional columns: - 'cl' : cluster number - 'dist_to_cent' : distance to cluster center. Documentation

Cheminformatics

• Improvements have been made to hierarchical grouping in tables. Documentation

Graphics

• Surface and pocket meshes are now grouped and linked directly to the ligand object.

September 1st 2014: Version 3.8-1 Released

New features include:

Modeling

• MERSi: Mutation Effects with Relaxation of Side-chains in Internal coordinates.
• Build homology models with rigorous refinement in batch (see Homology/Batch Build and Refine).
• Loop Grafting - transfer a loop region from one protein to another. Documentation
• Build peptides and make mutations using unusual amino acids. A table of 250 non-standard Amino Acids added and enabled for the mutation tool.
• Protein Sculpting can be used to model the interaction of two connected domains. You simply drag the molecules around a hinge region followed by a minimization. Documentation

Sequence and Alignment

• Calculate Global or Local Sequence Similarity and Identity in an Alignment. Documentation
• Sequence drag'n'drop between sessions is now supported.
• Multi-line sequence alignment annotations are now supported.

Cheminformatics

• Extensive chemical dictionary is now available in the molecule editor.
• Direct search of the Crystallography Open Database (COD). The COD is an open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers.
• Direct interface in GUI for searching PubChem. Documentation
• Match chemical 2D sketch to PubChem and extract PubChem CID or ID number (Use Insert Column and choose Function Chemical PubChem).
• New set of pre-prepared common covalent binding mechanism reactions for covalent ligand docking. Documentation

February 5th 2014: MolSoft Releases New ICM Version 3.8

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

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.

• More information here: http://www.molsoft.com/molscreen.html
• Documentation here: http://www.molsoft.com/gui/molscreen.html
• Please download the latest ICM version here: http://www.molsoft.com/support

March 7th 2012: ICM Version 3.7 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..]

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