BIPSPI: a method for the prediction of partner-specific protein-protein interfaces

Bioinformatics
Ruben Sanchez-GarciaJoan Segura

Abstract

Protein-Protein Interactions (PPI) are essentials for most cellular processes and thus, unveiling how proteins interact is a crucial question that can be better understood by identifying which residues are responsible for the interaction. Computational approaches are orders of magnitude cheaper and faster than experimental ones, leading to proliferation of multiple methods aimed to predict which residues belong to the interface of an interaction. We present BIPSPI, a new machine learning-based method for the prediction of partner-specific PPI sites. Contrary to most binding site prediction methods, the proposed approach takes into account a pair of interacting proteins rather than a single one in order to predict partner-specific binding sites. BIPSPI has been trained employing sequence-based and structural features from both protein partners of each complex compiled in the Protein-Protein Docking Benchmark version 5.0 and in an additional set independently compiled. Also, a version trained only on sequences has been developed. The performance of our approach has been assessed by a leave-one-out cross-validation over different benchmarks, outperforming state-of-the-art methods. BIPSPI web server is freely available at http://bi...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 29, 1997·Journal of Molecular Biology·F PazosA Valencia
Dec 31, 2002·Current Opinion in Structural Biology·Frank Sobott, Carol V Robinson
Apr 22, 2003·Statistics in Medicine·Jerome H Friedman, Jacqueline J Meulman
Jun 5, 2003·Proteins·Joël JaninUNKNOWN Critical Assessment of PRedicted Interactions
Jul 11, 2003·Nucleic Acids Research·Andrei Grigoriev
Mar 31, 2004·Journal of Molecular Biology·Hani NeuvirthGideon Schreiber
Feb 2, 2006·Proteins·Sjoerd J de VriesAlexandre M J J Bonvin
Dec 8, 2006·Proteins·Aleksey Porollo, Jarosław Meller
Nov 15, 2007·Nucleic Acids Research·Antonina AndreevaAlexey G Murzin
Jan 17, 2008·Biochemistry·Daping FanSergio Fazio
Apr 11, 2008·BMC Structural Biology·Josip MihelKristian Vlahovicek
May 21, 2008·Proteins·Howook HwangZhiping Weng
Jan 31, 2009·PLoS Computational Biology·Mile SikićKristian Vlahovicek
Oct 17, 2009·Proteomics·Mitchell R O'ConnellJoel P Mackay
Sep 2, 2010·Proteins·Howook HwangZhiping Weng
Aug 25, 2011·BMC Bioinformatics·Joan SeguraNarcis Fernandez-Fuentes
May 9, 2012·Bioinformatics·Joan SeguraNarcis Fernandez-Fuentes
Feb 13, 2013·Nature Methods·Roberto MoscaPatrick Aloy
May 30, 2013·Current Pharmaceutical Design·Jing ChenLuhua Lai
Nov 19, 2013·Proteins·Fayyaz ul Amir Afsar MinhasAsa Ben-Hur
Feb 28, 2014·Methods in Molecular Biology·Faruck MorcosMartin Weigt
Jun 12, 2014·The Journal of Pharmacology and Experimental Therapeutics·Tracy MitchellRex A Parker
Oct 22, 2014·Methods in Molecular Biology·João P G L M RodriguesAlexandre M J J Bonvin
Mar 13, 2015·PloS One·Joan SeguraNarcis Fernandez-Fuentes
Jul 17, 2015·Protein Science : a Publication of the Protein Society·Howook HwangBarry Honig
Jan 14, 2016·Current Drug Targets·Qian ZhangTingjun Hou
Jan 17, 2016·Biophysical Journal·Joan SeguraJose Maria Carazo
Feb 14, 2016·Journal of Structural Biology·D Tabas-MadridJ M Carazo
Jan 29, 2017·Bioinformatics·Castrense SavojardoRita Casadio
Jun 3, 2017·Bioinformatics·J JiménezG De Fabritiis
Jun 3, 2017·Current Opinion in Structural Biology·T M CafarelliM Vidal
Dec 16, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Ruben Sanchez-GarciaJoan Segura
Jan 23, 2018·Nature Methods·Michael J MeyerHaiyuan Yu

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Citations

Oct 2, 2020·PloS One·Grijesh Jaiswal, Veerendra Kumar
Mar 2, 2021·Journal of Biomolecular Structure & Dynamics·Grijesh JaiswalVeerendra Kumar
Mar 12, 2021·Briefings in Bioinformatics·Yumeng Yan, Sheng-You Huang
Mar 12, 2021·Bioinformatics·Bowen Dai, Chris Bailey-Kellogg
Jun 30, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Ayesha Z BegAsad U Khan
Oct 29, 2021·PLoS Neglected Tropical Diseases·Alejandro L AntoniaDennis C Ko
Nov 18, 2021·The Protein Journal·Sharon Sunny, P B Jayaraj

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Methods Mentioned

BETA
X-ray
nuclear magnetic resonance

Software Mentioned

PSAIA
xgBoost Interface
AL2CO
BIPSPI
ECLAIR
ELIXIR
Extreme
ISPRED4
Random Forest
Biopython

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