Docking of small ligands to low-resolution and theoretically predicted receptor structures

Journal of Computational Chemistry
Marek Wojciechowski, Jeffrey Skolnick

Abstract

We have developed a simple docking procedure that is able to utilize low-resolution models of proteins created by structure prediction algorithms such as threading or ab initio folding to predict the conformation of receptor-small ligand complexes. In our approach, using only approximate, discretized models of both molecules, we search for the steric and quasi-chemical complementarity between a ligand and the receptor molecules. This averaging procedure allows for the compensation of numerous structural inaccuracies resulting from the theoretical predictions of the receptor structure. The best relative orientation of these two models is obtained by an exhaustive scan over the rigid body's six-dimensional translational and rotational degrees of freedom. The search method is based on a real space grid-searching algorithm, unlike docking methods based on the fast Fourier Transform algorithm. We have applied this algorithm to rebuild structures of several complexes available in the Protein Data Bank. The structures of the receptors are produced by means of our threading algorithm PROSPECTOR, subsequently refined, and then utilized in the docking experiment. In many cases, not only is the localization of the binding site on the rece...Continue Reading

References

May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Jan 1, 1992·Faraday Discussions·G E Schulz
Mar 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·E Katchalski-KatzirI A Vakser
May 5, 1991·Journal of Molecular Biology·F Jiang, S H Kim
Oct 25, 1982·Journal of Molecular Biology·I D KuntzT E Ferrin
Apr 1, 1995·Protein Engineering·I A Vakser
Jan 7, 1994·Journal of Molecular Biology·A R Leach
Apr 1, 1996·Protein Science : a Publication of the Protein Society·Z WengC Delisi
Aug 1, 1996·Journal of Computer-aided Molecular Design·G M MorrisA J Olson
Mar 1, 1996·Journal of Molecular Recognition : JMR·D A GschwendI D Kuntz
Nov 22, 1996·Journal of Molecular Biology·M MeyerD Schomburg
Feb 1, 1997·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·J DesmetI Lasters
Sep 23, 1997·Journal of Molecular Biology·H A GabbM J Sternberg
Jul 8, 1998·Proceedings of the National Academy of Sciences of the United States of America·J Y Trosset, H A Scheraga
Jul 21, 1999·Proceedings of the National Academy of Sciences of the United States of America·I A VakserC F Lam
Jan 29, 2000·Proteins·A KolinskiJ Skolnick
Feb 28, 2001·Proceedings of the National Academy of Sciences of the United States of America·J PillardyH A Scheraga

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Citations

Sep 23, 2003·Journal of Molecular Biology·Michael SilbersteinSandor Vajda
Jul 23, 2002·Current Opinion in Chemical Biology·Heather A Carlson
Sep 22, 2010·Journal of Chemical Information and Modeling·Michal Brylinski, Jeffrey Skolnick
Mar 28, 2009·Briefings in Bioinformatics·Jeffrey Skolnick, Michal Brylinski
Jun 9, 2009·PLoS Computational Biology·Michal Brylinski, Jeffrey Skolnick
Feb 23, 2008·Journal of Computational Chemistry·Michal Brylinski, Jeffrey Skolnick
Oct 15, 2009·Journal of Computational Chemistry·Michal Brylinski, Jeffrey Skolnick
Jan 15, 2005·Journal of Computational Chemistry·Eckart Bindewald, Jeffrey Skolnick

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