Predicting the protein-protein interactions using primary structures with predicted protein surface.

BMC Bioinformatics
Darby Tien-Hao ChangPo-Chang Lin

Abstract

Many biological functions involve various protein-protein interactions (PPIs). Elucidating such interactions is crucial for understanding general principles of cellular systems. Previous studies have shown the potential of predicting PPIs based on only sequence information. Compared to approaches that require other auxiliary information, these sequence-based approaches can be applied to a broader range of applications. This study presents a novel sequence-based method based on the assumption that protein-protein interactions are more related to amino acids at the surface than those at the core. The present method considers surface information and maintains the advantage of relying on only sequence data by including an accessible surface area (ASA) predictor recently proposed by the authors. This study also reports the experiments conducted to evaluate a) the performance of PPI prediction achieved by including the predicted surface and b) the quality of the predicted surface in comparison with the surface obtained from structures. The experimental results show that surface information helps to predict interacting protein pairs. Furthermore, the prediction performance achieved by using the surface estimated with the ASA predictor...Continue Reading

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Citations

Jun 4, 2013·Journal of Molecular Modeling·Brijesh K SriwastavaDariusz Plewczynski
Jun 1, 2012·Expert Opinion on Drug Discovery·Matthew JessulatAshkan Golshani
Jan 2, 2013·Gene·Chen-Yu FanDarby Tien-Hao Chang
Nov 12, 2016·Journal of Theoretical Biology·Pablo MierMiguel A Andrade-Navarro
Jun 15, 2018·Scientific Reports·S M Ashiqul IslamErich J Baker
Dec 19, 2015·Molecular Systems Biology·Jamie SniderIgor Stagljar
Mar 24, 2017·Briefings in Bioinformatics·Jian Zhang, Lukasz Kurgan

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Methods Mentioned

BETA
RSA

Software Mentioned

PSI
LIBSVM
DSSP
Dictionary of Protein Secondary Structure ( DSSP )
RVKDE
BLAST

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