Newsletter July 2008

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 oct08 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