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Overview of Key ICM Features. NIBR - Emeryville July 10-11 2012. Introduction to MolSoft. Established in 1994 Privately owned Worldwide customer base in academia, pharma and biotech Many published success stories in comp bio & chem. Support. E-mail [email protected]

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Overview of key icm features

Overview of Key ICM Features

NIBR - Emeryville

July 10-11 2012

Introduction to molsoft
Introduction to MolSoft

  • Established in 1994

  • Privately owned

  • Worldwide customer base in academia, pharma and biotech

  • Many published success stories in comp bio & chem



[email protected]

[email protected]


858-625-2000 x108


Molecule visualization
Molecule Visualization

  • Store in a single file:

    • Representations

    • Lighting/Depth

    • Multiple Slides

    • Multiple Viewpoints

    • Annotation

    • Rendering

    • Parametric Animations

    • Alignments

    • Chemical Tables

Product: ICM-Browser & ActiveICM

Imolview for the ipad and iphone
iMolview for the iPad and iPhone


  • Fully interactive alignments

  • Trees

  • Sequence and alignments directly linked to 3D structure

  • Rich alignment editor

  • Sequence search PDB, Uniprot etc…

Structure analysis
Structure Analysis

  • Calculate

    • RMSD

    • Contact Areas

    • Surface Areas

    • Measure distances and angles (planar, dihedral)

    • Fully interactive Ramachandran Plots

    • Protein Superposition

Structure prediction
Structure Prediction

  • Identify closed cavities

  • Identify ligand binding sites (An et al 2005 & Kufareva et al 2012)

  • Identify protein-protein interaction sites (Fernandez-Recio et al 2005)

  • Protein health

An, J., Totrov, M., and Abagyan, R. (2005). Pocketome Via Comprehensive Identification and Classification of Ligand Binding Envelopes. Mol Cell Proteomics 4, 752–761.

  • Kufareva I, Ilatovskiy AV, Abagyan R. Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res. 2012 Jan;40(Database issue):D535-40.

  • Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins. 2005 Jan 1;58(1):134-43

Crystallographic analysis
Crystallographic Analysis

  • Neighbors

  • Cell

  • Biomolecule generator

  • Display and contour electron density maps

Homology modeling
Homology Modeling

  • Build homology models (Katritch et al 2010)

  • Refine models

  • Predict and/or design loop conformation

  • Search loop databases

  • New loop modeling force-field (Arnautova et al 2011)

Arnautova YA, Abagyan RA, Totrov M. Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins. 2011 Feb;79(2):477-98.

  • Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R. GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins. 2010 Jan;78(1):197-211

3d interactive ligand editor
3D Interactive Ligand Editor

  • Interactively edit a ligand bound to a receptor in 3D.

  • Screen for best replacement group

  • Join fragments by linkers.

  • Edit ligand in 2D molecular editor.

  • Delete atoms and bonds.

  • Convenient undo and redo modification feature.

  • Dock and/or minimize edited ligand.

  • Fragment docking.

  • Multiple receptor docking

  • Restrain atoms during docking


  • 2D ligand sketcher

  • Fully interactive chemical spreadsheets and plots

  • Chemical clustering

  • Chemical searching

  • Library enumeration

  • Pharmacophore searching

Atomic property fields
Atomic Property Fields

A continuous, multi-component 3D potential that reflects preferences for various atomic properties at each point in space.

Totrov M. Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites. BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S35.

Grigoryan AV, Kufareva I, Totrov M, Abagyan RA. Spatial chemical distance based on atomic property fields. J Comput Aided Mol Des. 2010 Mar;24(3):173-82.

Totrov M. Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. ChemBiol Drug Des. 2008 Jan;71(1):15-27.

Docking screening
Docking & Screening

  • Small molecule docking

  • Protein-protein docking

  • Template docking

  • Induced Fit Docking

    • Multiple Receptors

    • Explicit Groups

  • Tethered Docking

  • Virtual Screening

    • Structure-based

    • Ligand- based APF

See: www.molsoft.com/vls

for success stories


  • What is it?

    • A single, unified client for data entry, mining and manipulation built into a powerful chemistry and bio-enabled platform

  • Prerequisites

    • One or multiple (possibly existing) relational databases with research data related to biology and chemistry

  • Deployment

    • A cross-platform client

    • Installs transparently on top of existing databases