Protein–protein interactions: scoring schemes and binding affinity

•Reviewed scoring schemes and conformational sampling for protein–protein complex structure prediction.•Discussed the database for binding affinity of complexes and mutants.•Covered both structural and sequence based approaches for understanding binding affinity.•Compiled the methods for predicting...

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Bibliographic Details
Published in:Current opinion in structural biology 2017-06, Vol.44, p.31-38
Main Authors: Gromiha, M Michael, Yugandhar, K, Jemimah, Sherlyn
Format: Article
Language:English
Subjects:
Humans
Mutation
Protein Binding
Protein Conformation
Protein Interaction Mapping - methods
Proteins - chemistry
Proteins - genetics
Proteins - metabolism
Thermodynamics
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Summary:•Reviewed scoring schemes and conformational sampling for protein–protein complex structure prediction.•Discussed the database for binding affinity of complexes and mutants.•Covered both structural and sequence based approaches for understanding binding affinity.•Compiled the methods for predicting binding affinity upon mutation.•Listed available resources on docking and binding affinity prediction. 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.
ISSN:0959-440X
1879-033X
DOI:10.1016/j.sbi.2016.10.016