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Bioinformatics Advance Access published online on March 7, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn093
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

3D-Garden: A system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

Victor I. Lesk 1,* and Michael J. E. Sternberg 1

1Division of Molecular Biosciences, Imperial College London, South Kensington, London SW72AZ, United Kingdom

*To whom correspondence should be addressed. Dr. Victor I. Lesk, E-mail: v.lesk{at}ic.ac.uk


  Abstract

Motivation: Reliable structural modelling of protein-protein complexes has widespread application, from drug design to advancing our knowledge of protein interactions and function. This work addresses three important issues in protein-protein docking: implementing backbone flexibility, incorporating prior indications from experiment and bioinformatics, and providing public access via a server. 3D-Garden, our benchmarked and server-ready flexible docking system, allows sophisticated programming of surface patches by the user via a facet representation of the interactors' molecular surfaces (generated with the marching cubes algorithm). Flexibility is implemented as a weighted exhaustive conformer search for each clashing pair of molecular branches in a set of 5000 models filtered from around ~340,000 initially.

Results: In a non-global assessment, carried out strictly according to the protocols for number of models considered and model quality of the CAPRI experiment, over the widely-used Benchmark 2.0 of 84 complexes, 3D-Garden identifies a set of ten models containing an acceptable or better model in 29/45 test cases, including one with large conformational change. In 19/45 cases an acceptable or better model is ranked first or second out of 340,000 candidates.

Availability: http://www.sbg.bio.ic.ac.uk/3dgarden (server)

Contact: v.lesk{at}ic.ac.uk

Associate Editor: Prof. Burkhard Rost

Received on November 27, 2007; revised on February 19, 2008; accepted on March 5, 2008

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S. E. Dobbins, V. I. Lesk, and M. J. E. Sternberg
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking
PNAS, July 29, 2008; 105(30): 10390 - 10395.
[Abstract] [Full Text] [PDF]


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