Gromiha MM, Yugandhar K, Jemimah S. Protein-protein interactions: scoring schemes and binding affinity.
Curr Opin Struct Biol 2016;
44:31-38. [PMID:
27866112 DOI:
10.1016/j.sbi.2016.10.016]
[Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/30/2016] [Accepted: 10/25/2016] [Indexed: 01/16/2023]
Abstract
Protein-protein interactions mediate several cellular functions, which can be understood from the information obtained using the three-dimensional structures of protein-protein complexes and binding affinity data. This review focuses on computational aspects of predicting the best native-like complex structure and binding affinities. The first part covers the prediction of protein-protein complex structures and the advantages of conformational searching and scoring functions in protein-protein docking. The second part is devoted to various aspects of protein-protein interaction thermodynamics, such as databases for binding affinities and other thermodynamic parameters, computational methods to predict the binding affinity using either the three-dimensional structures of complexes or amino acid sequences, and change in binding affinities of the complexes upon mutations. We provide the latest developments on protein-protein docking and binding affinity studies along with a list of available computational resources for understanding protein-protein interactions.
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