iAlign: a method for the structural comparison of protein-protein interfaces.

Bioinformatics
Mu Gao, Jeffrey Skolnick

Abstract

Protein-protein interactions play an essential role in many cellular processes. The rapid accumulation of protein-protein complex structures provides an unprecedented opportunity for comparative studies of protein-protein interactions. To facilitate such studies, it is necessary to develop an accurate and efficient computational algorithm for the comparison of protein-protein interaction modes. While there are many structural comparison approaches developed for individual proteins, very few methods are available for protein-protein complexes. We present a novel interface alignment method, iAlign, for the structural alignment of protein-protein interfaces. New scoring schemes for measuring interface similarity are introduced, and an iterative dynamic programming algorithm is implemented. We find that the similarity scores follow extreme value distributions. Using statistical models, we empirically estimate their statistical significance, which is in good agreement with manual classifications by human experts. Large-scale tests of iAlign were conducted on both artificial docking models and experimental structures. In a benchmark test on 1517 dimers, iAlign successfully detects biologically related, structurally similar protein-pr...Continue Reading

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Citations

Apr 18, 2013·Journal of Proteome Research·Guray KuzuOzlem Keskin
Jun 10, 2011·Physical Chemistry Chemical Physics : PCCP·Michal BrylinskiJeffrey Skolnick
Mar 28, 2013·Molecular BioSystems·Anshul Sukhwal, Ramanathan Sowdhamini
Dec 15, 2010·Proceedings of the National Academy of Sciences of the United States of America·Mu Gao, Jeffrey Skolnick
Feb 23, 2012·Proceedings of the National Academy of Sciences of the United States of America·Mu Gao, Jeffrey Skolnick
Dec 20, 2012·Journal of Biomolecular Structure & Dynamics·Ramachandra M BhaskaraNarayanaswamy Srinivasan
Aug 30, 2011·Bioinformatics·Anisah W GhoorahDavid W Ritchie
Apr 12, 2012·Bioinformatics·Bin PangChi-Ren Shyu
Jan 22, 2013·Bioinformatics·Mu Gao, Jeffrey Skolnick
Jun 13, 2012·Nucleic Acids Research·Bin PangChi-Ren Shyu
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Jan 13, 2016·BMC Bioinformatics·Nithin ShivashankarVijay Natarajan
Mar 15, 2013·Scientific Reports·Sheng WangJinbo Xu
Mar 3, 2011·Proteins·Mu Gao, Jeffrey Skolnick
Jul 20, 2011·The FEBS Journal·Ritcha Mehra-ChaudharyLesa J Beamer
Dec 1, 2013·Molecular Informatics·Xavier Jalencas, Jordi Mestres
Dec 9, 2014·Israel Journal of Chemistry·Jeffrey SkolnickHongyi Zhou
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Jun 3, 2015·Journal of Chemical Information and Modeling·Florian KrullErnst-Walter Knapp
Feb 2, 2015·BMC Bioinformatics·Shanshan ChengCharles L Brooks
Mar 7, 2017·Proteins·Claudio Mirabello, Björn Wallner
Jan 27, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Norman GoodacreCathy Wu
Mar 11, 2016·F1000Research·Jeffrey SkolnickHongyi Zhou
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Nov 14, 2018·Bioinformatics·Claudio Mirabello, Björn Wallner
Jun 9, 2021·Nature Communications·Sony MalhotraMaya Topf
Sep 30, 2021·Journal of Chemical Information and Modeling·Jeffrey SkolnickSuresh Singh

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