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Protein-protein docking: Progress in CAPRI rounds 6-12 using a combination of methods: The introduction of steered solvated molecular dynamics

Lookup NU author(s): Dr Sandeep Pal, Dr Graham Smith


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In recent rounds of CAPRI, the Bii group has employed a combination of techniques for the prediction of the structure of protein-protein complexes. We currently use third-party software for rigid-body and semiflexible docking (MolFit, 3D-Dock, RosettaDock), and our own steered molecular dynamics (SMD) technique for flexible refinement. SMD has also been found to be useful for discriminating near-native from false positive docking decoys. In addition to this, a variety of sources of information, including multiple descriptors of interface quality combined with a QSAR-like technique, published biological information, and continuum electrostatics calculations, are also used in the assessment of candidate complexes. We shall concentrate on results for CAPRI rounds 9-11 (targets 24-27). In these rounds, the Bii group has been successful in submitting a medium quality model for each of CAPRI targets 25 and 26, and a model of acceptable quality for target 27.

Publication metadata

Author(s): Heifetz A, Pal S, Smith GR

Publication type: Conference Proceedings (inc. Abstract)

Publication status: Published

Conference Name: Third Meeting on the Critical Assessment of Predicted Interactions

Year of Conference: 2007

Pages: 816-822

ISSN: 0887-3585

Publisher: Proteins: Structure, Function, and Bioinformatics, Wiley-Blackwell


DOI: 10.1002/prot.21734

Library holdings: Search Newcastle University Library for this item

ISBN: 10970134