Flexible protein-protein docking.

Alexandre M J J Bonvin

doi:10.1016/j.sbi.2006.02.002

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Flexible protein-protein docking.

Alexandre M J J Bonvin

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Abstract

Predicting the structure of protein-protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutions, and properly dealing with molecular flexibility and conformational changes. Flexibility can be addressed at several levels: implicitly, by smoothing the protein surfaces or allowing some degree of interpenetration (soft docking) or by performing multiple docking runs from various conformations (cross or ensemble docking); or explicitly, by allowing sidechain and/or backbone flexibility. Although significant improvements have been achieved in the modeling of sidechains, methods for the explicit inclusion of backbone flexibility in docking are still being developed. A few novel approaches have emerged involving collective degrees of motion, multicopy representations and multibody docking, which should allow larger conformational changes to be modeled.

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Alexandre M J J Bonvin. 2006-02-17. Flexible protein-protein docking.. https://doi.org/10.1016/j.sbi.2006.02.002

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