Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 11, Issue 10, Pages 3623-3648Publisher
MDPI
DOI: 10.3390/ijms11103623
Keywords
elastic network model; normal mode analysis; particle swarm optimisation; PSO; protein flexibility; RTB; CAPRI
Funding
- Cancer Research UK
- Cancer Research UK [10748] Funding Source: researchfish
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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.
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