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Bioinformatics Advance Access originally published online on March 7, 2008
Bioinformatics 2008 24(9):1137-1144; 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 * and Michael J. E. Sternberg

Division of Molecular Biosciences, Imperial College London, South Kensington, London SW72AZ, UK

*To whom correspondence should be addressed.


  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 (Global And Restrained Docking Exploration Nexus), 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 Critical Assessment of Protein Interactions (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

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rost

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

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