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SwarmDock and the use of normal modes in protein-protein docking.

ABSTRACT: Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.

SUBMITTER: Moal IH

PROVIDER: S-EPMC2996808 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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SwarmDock and the use of normal modes in protein-protein docking.

Moal Iain H IH Bates Paul A PA

International journal of molecular sciences 20100928 10

Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combinatio ...[more]

PMID: 21152290

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