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PEDS Advance Access published online on February 15, 2005
Protein Engineering Design and Selection, doi:10.1093/protein/gzh100
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org
Received August 15, 2004
Revised October 22, 2004
Accepted December 28, 2004

Article

Incorporating intermolecular distance into protein-protein docking

Hongxing Lei 1 and Yong Duan 1*

1 UC Davis Genome Center and Bioinformatics Program, Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616, USA

* To whom correspondence should be addressed.
Yong Duan, E-mail: duan{at}ucdavis.edu


  Abstract

In this work, intermolecular distance was integrated into the docking of protein-protein complexes. To develop an efficient docking procedure, 22 enzyme-inhibitor targets and 15 antibody-antigen targets were taken from a benchmark set. A three-step approach was adopted, which included global sampling by FTDOCK, filtering by intermolecular distance and ranking by a composite scoring function. For the enzyme-inhibitor targets, the composite scoring function consists of geometry and energy terms. In the set composed of the ~100 highest ranked candidates for each target, correct complexes were identified for all of the 22 enzyme-inhibitor targets. This docking strategy also succeeded on the four test targets, of which three are CAPRI targets with the same receptor but different binding modes. Interestingly, all three binding modes were correctly predicted. For the antibody-antigen targets, CDR and physical energy were also used in the filtering process and informatics terms were added to the scoring function. The composite score had successful prediction for 13 of the 15 antibody-antigen targets.

Keywords: antibody-antigen; enzyme inhibitor; intermolecular distance; protein-protein docking.
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