Overview

This lesson will take you through the basics of protein modeling. Topics include:

• Building a homology model.
• Linked alignments and structures.
• Protein health and regularization.
• Protein folding and structure prediction.

Background

ICM has an excellent record in building accurate models by homology. The ICM modeling procedure builds the framework, shakes up the side-chains and loops by global energy optimization. You can also color the model by local reliability to identify the potentially wrong parts of the model. ICM also offers a fast and completely automated method to build a model by homology and extract the best fitting loops from a database of all known loops. It just takes a few seconds to build a complete model by homology with loops. Some selected publications related to modeling and structure determination are listed here.

Abagyan, R.A., and Totrov, M.M. (1994). Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins. J. Mol. Biol., 235, 983-1002

Cardozo, T., Totrov, M., and Abagyan, R. (1995). Homology modeling by the ICM method. Proteins: Structure, Function, Genetics, 23, 403-414

Abagyan, R., and Totrov, M. (1999). Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure. Journal of Computational Physics, 151, 402-421

Maiorov, V.N., and Abagyan, R.A. (1997). A new method for modeling large-scale rearrangements of protein domains. Proteins, 27, 410-424

Schapira, M., Totrov, M. and Abagyan, R. (2002). Structural Model of Nicotinic Acetylcholine Receptor Isotypes Bound to cetylcholine and Nicotine. BMC Structural Biology 2:1

ICM also provides powerful tools for determining crystallographic symmetry and neighbors which allows the biological environment of a protein to be viewed and understood.