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.
Journal details
Volume 11
Issue number 10
Pages 3623-3648
Publication date
Full text links
Publisher website (DOI) 10.3390/ijms11103623
Europe PubMed Central 21152290
Pubmed 21152290
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