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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 andy@molsoft.com

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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





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

  • 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