Overview

ICM provides a unique set of tools for the modeling of protein/ligand interactions. The algorithm performs fast and accurate docking of fully continuously flexible small molecule ligands to a protein represented by grid interaction potentials. The algorithm performs exceptionally well compared to other docking algorithms on the market (see Bursulaya et al 2004 Journal of Computer Aided Molecular Design). The algorithm has been developed to incorporate flexibility into the receptor binding pocket to mimic the induced-fit caused when a ligand binds with a receptor (see Cavasotto and Abagyan Journal of Molecular Biology 2004). <>

ICM docking has been used to solve many drug-design problems and here is a select list of references.

Schapira, M., Raaka, B.M., Samuels, H, H. and Abagyan, R. (2000). Rational discovery of novel nuclear hormone receptor antagonists. PNAS, Feb 1;97 (3), 1008-1013

Abagyan, R. and Totrov, M. (2001). High-throughput Docking for Lead Generation. Current Opinion in Chemical Biology. Aug;5(4):375-82

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

Cavasotto, C., Orry, A.J.W., Abagyan, R. (2003). Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors. Proteins: Structure, Function, and Genetics 51(3), 423-433

Bursulaya BD, Totrov M, Abagyan R, Brooks CL 3rd.Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des. 2003 Nov;17(11):755-63.

Cavasotto CN, Abagyan RA. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol. 2004 Mar 12;337(1):209-25.

Altmann SM, Muryshev A, Fossale E, Maxwell MM, Norflus FN, Fox J, Hersch SM, Young AB, MacDonald ME, Abagyan R, Kazantsev AG. Discovery of bioactive small-molecule inhibitor of poly adp-ribose polymerase: implications for energy-deficient cells. Chem Biol. 2006 Jul;13(7):765-70.

Cavasotto CN, Ortiz MA, Abagyan RA, Piedrafita FJ. In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells. Bioorg Med Chem Lett. 2006 Jan 11