ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein–protein complexes upon mutation using functional classification

Sherlyn  Jemimah; Masakazu Sekijima; Michael Gromiha

doi:https://doi.org/10.1093/bioinformatics/btz829

Publication Information

Title

Japanese:	ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein–protein complexes upon mutation using functional classification
English:	ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein–protein complexes upon mutation using functional classification

Author

Japanese:	Sherlyn Jemimah, 関嶋政和, MARIASILUVAY MICHAEL GROMIHA.
English:	Sherlyn Jemimah, Masakazu Sekijima, Michael Gromiha.

Language

English

Journal/Book name

Japanese:	Bioinformatics
English:	Bioinformatics

Volume, Number, Page

Published date

Nov. 12, 2019

Publisher

Japanese:
English:

Conference name

Japanese:
English:

Conference site

Japanese:
English:

Official URL

http://dx.doi.org/10.1093/bioinformatics/btz829

DOI

https://doi.org/10.1093/bioinformatics/btz829

Abstract

Abstract Motivation Protein–protein interactions are essential for the cell and mediate various functions. However, mutations can disrupt these interactions and may cause diseases. Currently available computational methods require a complex structure as input for predicting the change in binding affinity. Further, they have not included the functional class information for the protein–protein complex. To address this, we have developed a method, ProAffiMuSeq, which predicts the change in binding free energy using sequence-based features and functional class. Results Our method shows an average correlation between predicted and experimentally determined ΔΔG of 0.73 and mean absolute error (MAE) of 0.86 kcal/mol in 10-fold cross-validation and correlation of 0.75 with MAE of 0.94 kcal/mol in the test dataset. ProAffiMuSeq was also tested on an external validation set and showed results comparable to structure-based methods. Our method can be used for large-scale analysis of disease-causing mutations in protein–protein complexes without structural information. Availability and implementation Users can access the method at https://web.iitm.ac.in/bioinfo2/proaffimuseq/. Supplementary information Supplementary data are available at Bioinformatics online.

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