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  A Combinatorial Approach to Protein Docking with Flexible Side-Chains

Althaus, E., Kohlbacher, O., Lenhof, H.-P., & Müller, P. (2000). A Combinatorial Approach to Protein Docking with Flexible Side-Chains. In R. Shamir, S. Miyano, S. Istrail, P. Pevzner, & M. Waterman (Eds.), Proceedings of the 4th Annual International Conference on Computational Molecular Biology (RECOMB-00) (pp. 15-24). New York, USA: ACM Press.

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 Creators:
Althaus, E, Author
Kohlbacher, O1, Author           
Lenhof, H-P, Author
Müller, P, Author
Affiliations:
1External Organizations, ou_persistent22              

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 Abstract: Rigid body docking approaches are not sufficient to predict the structure of a protein complex from the unbound (native) structures of the two proteins. Accounting for side—chain flexibility is an important step towards fully flexible protein docking. This work describes an approach that allows conformational flexibility for the side—chains while keeping the protein backbone rigid. Starting from candidates created by a rigid docking algorithm, we demangle the side—chains of the docking site, thus creating reasonable approximations of the true complex structure. These structures are ranked with respect to the binding free energy. We present two new techniques for side—chain demangling. Both approaches are based on a discrete representation of the side—chain conformational space by the use of a rotamer library. This leads to a combinatorial optimization problem. For the solution of this problem we propose a fast heuristic approach and an exact, albeit slower method using branch—&—cut techniques. As a test set we use the unbound structures of three proteases and the corresponding protein inhibitors. For each of the examples the highest—ranking conformation produced was a good approximation of the true complex structure.

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Language(s): eng - English
 Dates: 2000-04
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1145/332306.332319
 Degree: -

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Title: Fourth Annual International Conference on Computational Molecular Biology (RECOMB 2000)
Place of Event: Tokyo, Japan
Start-/End Date: 2000-04-08 - 2000-04-11

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Title: Proceedings of the 4th Annual International Conference on Computational Molecular Biology (RECOMB-00)
Source Genre: Proceedings
 Creator(s):
Shamir, R, Editor
Miyano, S, Editor
Istrail, S, Editor
Pevzner, P, Editor
Waterman, M, Editor
Affiliations:
-
Publ. Info: New York, USA : ACM Press
Pages: 329 Volume / Issue: - Sequence Number: - Start / End Page: 15 - 24 Identifier: ISBN: 978-1-58113-186-4