PPIcons: identification of protein-protein interaction sites in selected organisms

Journal of Molecular Modeling
Brijesh K SriwastavaDariusz Plewczynski

Abstract

The physico-chemical properties of interaction interfaces have a crucial role in characterization of protein-protein interactions (PPI). In silico prediction of participating amino acids helps to identify interface residues for further experimental verification using mutational analysis, or inhibition studies by screening library of ligands against given protein. Given the unbound structure of a protein and the fact that it forms a complex with another known protein, the objective of this work is to identify the residues that are involved in the interaction. We attempt to predict interaction sites in protein complexes using local composition of amino acids together with their physico-chemical characteristics. The local sequence segments (LSS) are dissected from the protein sequences using a sliding window of 21 amino acids. The list of LSSs is passed to the support vector machine (SVM) predictor, which identifies interacting residue pairs considering their inter-atom distances. We have analyzed three different model organisms of Escherichia coli, Saccharomyces Cerevisiae and Homo sapiens, where the numbers of considered hetero-complexes are equal to 40, 123 and 33 respectively. Moreover, the unified multi-organism PPI meta-pred...Continue Reading

References

Nov 5, 1988·Journal of Molecular Biology·J JaninC Chothia
Jul 1, 1988·Protein Engineering·P Argos
Apr 1, 1988·Biophysical Chemistry·P Zielenkiewicz, A Rabczenko
Jan 21, 1994·Journal of Molecular Biology·M Helmer-Citterich, A Tramontano
Jan 1, 1995·Progress in Biophysics and Molecular Biology·S Jones, J M Thornton
Jan 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·S Jones, J M Thornton
Sep 23, 1997·Journal of Molecular Biology·S Jones, J M Thornton
Feb 2, 1999·Journal of Molecular Biology·L Lo ConteJ Janin
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Apr 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·T ItoY Sakaki
Mar 5, 2002·European Journal of Biochemistry·Piero FariselliRita Casadio
Apr 3, 2003·Nature Reviews. Neuroscience·James L McClelland, Timothy T Rogers
Dec 19, 2003·Nucleic Acids Research·Lukasz SalwinskiDavid Eisenberg
Mar 31, 2004·Journal of Molecular Biology·Hani NeuvirthGideon Schreiber
Sep 15, 2004·Journal of Molecular Biology·Vijayalakshmi ChelliahSimon C Lovell
Dec 23, 2004·Bioinformatics·James R Bradford, David R Westhead
Feb 11, 2005·Bioinformatics·Alasdair T R Laurie, Richard M Jackson
May 21, 2005·Proteins·Andrew J Bordner, Ruben Abagyan
Jan 24, 2006·Nature·Anne-Claude GavinGiulio Superti-Furga
Mar 24, 2006·Nature·Nevan J KroganJack F Greenblatt
May 26, 2006·BMC Bioinformatics·Asa Ben-Hur, William Stafford Noble
Aug 9, 2006·Nucleic Acids Research·Shide LiangYaoqi Zhou
Dec 8, 2006·Proteins·Aleksey Porollo, Jarosław Meller
Sep 4, 2007·Psychosomatic Medicine·Desta B FekedulegnDiane B Miller
Sep 27, 2007·Bioinformatics·Sanbo Qin, Huan-Xiang Zhou
Jan 21, 2009·Bioinformatics·Xue-wen Chen, Jong Cheol Jeong
Dec 18, 2009·BMC Bioinformatics·Lei DengShuigeng Zhou
Apr 29, 2010·BMC Bioinformatics·Subhadip Basu, Dariusz Plewczynski
Sep 22, 2010·Journal of Molecular Modeling·Dariusz Plewczynski
Mar 29, 2011·Cellular & Molecular Biology Letters·Piyali ChatterjeeDariusz Plewczynski
Oct 14, 2011·Amino Acids·Indrajit SahaDariusz Plewczynski
Dec 28, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Clara Pizzuti, Simona E Rombo
Feb 15, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Debarka SenguptaSanghamitra Bandyopadhyay

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Citations

Dec 20, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Brijesh K SriwastavaUjjwal Maulik
Sep 3, 2016·Bioinformatics·Olga S VoitenkoOlga V Kalinina
Feb 8, 2018·BMC Bioinformatics·Sebastian Daberdaku, Carlo Ferrari
Mar 29, 2020·International Journal of Molecular Sciences·Aijun DengBing Wang

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Methods Mentioned

BETA
X-ray
NMR
interaction sites prediction
interaction prediction
in silico methods

Software Mentioned

Cons
Struct2Net
DSSP
Promate
hfill
Apache
PPIcons

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