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Bioinformatics Advance Access published online on October 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti055
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received April 15, 2004
Revised June 10, 2004
Accepted September 26, 2004

Article

Improving conformational searches by geometric screening

Ming Zhang 1*, R. Allen White 1, Liqun Wang 2, Ronald Goldman 3, Lydia Kavraki 4, and Brendan Hassett 5

1 Department of Biostatistics and Applied Mathematics, The University of Texas M.D. Anderson Cancer Center, Houston TX 77030 USA; Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77225 USA
2 Department of Biostatistics and Applied Mathematics, The University of Texas M.D. Anderson Cancer Center, Houston TX 77030 USA
3 Department of Computer Science, Rice University, Houston TX 77251 USA
4 Department of Computer Science, Rice University, Houston TX 77251 USA; Department of Bioengineering, Rice University, Houston TX 77251 USA; Graudate Program in Structural & Computational Biology, Baylor College of Medicine, Houston TX 77030 USA
5 Department of Mathematics, Rice University, Houston TX 77251 USA

* To whom correspondence should be addressed. E-mail: mzhang{at}mdanderson.org.


  Abstract

Motivation: Conformational searches in molecular docking are a time-consuming process with wide range of applications. Favorable conformations of the ligands that successfully bind with receptors are sought to form stable ligand-receptor complexes. Usually a large number of conformations are generated and their binding energies are examined. We propose adding a geometric screening phase before an energy minimization procedure so that only conformations that geometrically fit in the binding site will be prompted for energy calculation.

Results: Geometric screening can drastically reduce the number of conformations to be examined from millions (or higher) to thousands (or lower). The method can also handle cases when there are more variables than geometric constraints. An early-stage implementation is able to finish the geometric filtering of conformations for molecules with up to nine variables in one minute. To the best of our knowledge, this is the first time such results are reported deterministically.


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