Workshop Guide

For more detailed description of the ICM methodology please see the ICM Graphical User Interface Manual (gui) or the ICM Command Line Manual (man). Please see our website for additional references and further reading.

Topic	Documentation	Selected References
How to Share and Communicate Structural Data		Raush et al. 2009, Abagyan et al. 2006
How to insert fully interactive structural data into PowerPoint.	gui
How to insert fully interactive structural data into a web page.	gui
Linking Sequence to Structure		Abagyan & Batalov 1997, Marsden & Abagyan 2004
Sequence alignment tools and algorithms.	gui/man
Linking sequence alignments to structure.	gui/man
Molecular Modeling		Abagyan & Totrov 1994, Abagyan et al. 1997
Choosing a template sequence.	man
How to build a molecular model.	gui/man
Evaluating a molecular model.	gui/man	Maiorov & Abagyan 1997
Model optimization procedures	man
Small Molecule Docking		Totrov & Abagyan 1994, Totrov & Abagyan 1997
Preparing a protein structure for docking.	man
Identifying small molecule binding sites.	gui/man	An et al. 2004
The ICM 3D Ligand Editor.	gui
Example: Biotin and the Streptavidin Receptor.	gui
Example: Inhibitor binding to Ricin.	gui
Chemical Biology
Working with Chemical Spreadsheets.	gui
Chemical Searching.	gui
Working with Pharmacophores.	gui	Totrov 2008
Chemical Clustering.	gui
Stereoisomers and Tautomers.	gui
Generating a combinatorial library.	gui	Orry et al. 2006
Virtual Ligand Screening		Bisson et al. 2007, Cavasotto et al. 2008, see other references here
Example: Virtual Ligand Screening to the Ricin Receptor	gui
Example: Virtual Screening of a Database of Cyclooxygenase Inhibitors.	gui
Example: Screening a Markush Library.	gui
Methods for Incorporating Receptor Flexibility into Docking and Screening		Kufareva & Abagyan 2008, Bottegoni et al. 2009, Bottegoni et al. 2008
Multiple Receptor Conformation	gui	Totrov & Abagyan 2008
Example: Multiple Receptor Conformation Ensemble Docking to Aldose Reductase	gui
Ligand Steered Docking		Abagyan & Kufareava 2009, Bisson et al. 2007