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  • Title: Protein-protein docking: progress in CAPRI rounds 6-12 using a combination of methods: the introduction of steered solvated molecular dynamics.
    Author: Heifetz A, Pal S, Smith GR.
    Journal: Proteins; 2007 Dec 01; 69(4):816-22. PubMed ID: 17803214.
    Abstract:
    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.
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