PPInS: a repository of protein-protein interaction sitesbase

Abstract Protein-Protein Interaction Sitesbase (PPInS), a high-performance database of protein-protein interacting interfaces, is presented. The atomic level information of the molecular interaction happening amongst various protein chains in protein-protein complexes (as reported in the Protein Dat...

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Autores principales:	Vicky Kumar, Suchismita Mahato, Anjana Munshi, Mahesh Kulharia
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/331bbcbde2ce4b41b4dd2bed90e0d9b1
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id	oai:doaj.org-article:331bbcbde2ce4b41b4dd2bed90e0d9b1
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spelling	oai:doaj.org-article:331bbcbde2ce4b41b4dd2bed90e0d9b12021-12-02T15:08:16ZPPInS: a repository of protein-protein interaction sitesbase10.1038/s41598-018-30999-12045-2322https://doaj.org/article/331bbcbde2ce4b41b4dd2bed90e0d9b12018-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-30999-1https://doaj.org/toc/2045-2322Abstract Protein-Protein Interaction Sitesbase (PPInS), a high-performance database of protein-protein interacting interfaces, is presented. The atomic level information of the molecular interaction happening amongst various protein chains in protein-protein complexes (as reported in the Protein Data Bank [PDB]) together with their evolutionary information in Structural Classification of Proteins (SCOPe release 2.06), is made available in PPInS. Total 32468 PDB files representing X-ray crystallized multimeric protein-protein complexes with structural resolution better than 2.5 Å had been shortlisted to demarcate the protein-protein interaction interfaces (PPIIs). A total of 111857 PPIIs with ~32.24 million atomic contact pairs (ACPs) were generated and made available on a web server for on-site analysis and downloading purpose. All these PPIIs and protein-protein interacting patches (PPIPs) involved in them, were also analyzed in terms of a number of residues contributing in patch formation, their hydrophobic nature, amount of surface area they contributed in binding, and their homo and heterodimeric nature, to describe the diversity of information covered in PPInS. It was observed that 42.37% of total PPIPs were made up of 6–20 interacting residues, 53.08% PPIPs had interface area ≤1000 Å2 in PPII formation, 82.64% PPIPs were reported with hydrophobicity score of ≤10, and 73.26% PPIPs were homologous to each other with the sequence similarity score ranging from 75–100%. A subset “Non-Redundant Database (NRDB)” of the PPInS containing 2265 PPIIs, with over 1.8 million ACPs corresponding to the 1931 protein-protein complexes (PDBs), was also designed by removing structural redundancies at the level of SCOP superfamily (SCOP release 1.75). The web interface of the PPInS (http://www.cup.edu.in:99/ppins/home.php) offers an easy-to-navigate, intuitive and user-friendly environment, and can be accessed by providing PDB ID, SCOP superfamily ID, and protein sequence.Vicky KumarSuchismita MahatoAnjana MunshiMahesh KulhariaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-9 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Vicky Kumar Suchismita Mahato Anjana Munshi Mahesh Kulharia PPInS: a repository of protein-protein interaction sitesbase
description	Abstract Protein-Protein Interaction Sitesbase (PPInS), a high-performance database of protein-protein interacting interfaces, is presented. The atomic level information of the molecular interaction happening amongst various protein chains in protein-protein complexes (as reported in the Protein Data Bank [PDB]) together with their evolutionary information in Structural Classification of Proteins (SCOPe release 2.06), is made available in PPInS. Total 32468 PDB files representing X-ray crystallized multimeric protein-protein complexes with structural resolution better than 2.5 Å had been shortlisted to demarcate the protein-protein interaction interfaces (PPIIs). A total of 111857 PPIIs with ~32.24 million atomic contact pairs (ACPs) were generated and made available on a web server for on-site analysis and downloading purpose. All these PPIIs and protein-protein interacting patches (PPIPs) involved in them, were also analyzed in terms of a number of residues contributing in patch formation, their hydrophobic nature, amount of surface area they contributed in binding, and their homo and heterodimeric nature, to describe the diversity of information covered in PPInS. It was observed that 42.37% of total PPIPs were made up of 6–20 interacting residues, 53.08% PPIPs had interface area ≤1000 Å2 in PPII formation, 82.64% PPIPs were reported with hydrophobicity score of ≤10, and 73.26% PPIPs were homologous to each other with the sequence similarity score ranging from 75–100%. A subset “Non-Redundant Database (NRDB)” of the PPInS containing 2265 PPIIs, with over 1.8 million ACPs corresponding to the 1931 protein-protein complexes (PDBs), was also designed by removing structural redundancies at the level of SCOP superfamily (SCOP release 1.75). The web interface of the PPInS (http://www.cup.edu.in:99/ppins/home.php) offers an easy-to-navigate, intuitive and user-friendly environment, and can be accessed by providing PDB ID, SCOP superfamily ID, and protein sequence.
format	article
author	Vicky Kumar Suchismita Mahato Anjana Munshi Mahesh Kulharia
author_facet	Vicky Kumar Suchismita Mahato Anjana Munshi Mahesh Kulharia
author_sort	Vicky Kumar
title	PPInS: a repository of protein-protein interaction sitesbase
title_short	PPInS: a repository of protein-protein interaction sitesbase
title_full	PPInS: a repository of protein-protein interaction sitesbase
title_fullStr	PPInS: a repository of protein-protein interaction sitesbase
title_full_unstemmed	PPInS: a repository of protein-protein interaction sitesbase
title_sort	ppins: a repository of protein-protein interaction sitesbase
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/331bbcbde2ce4b41b4dd2bed90e0d9b1
work_keys_str_mv	AT vickykumar ppinsarepositoryofproteinproteininteractionsitesbase AT suchismitamahato ppinsarepositoryofproteinproteininteractionsitesbase AT anjanamunshi ppinsarepositoryofproteinproteininteractionsitesbase AT maheshkulharia ppinsarepositoryofproteinproteininteractionsitesbase
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PPInS: a repository of protein-protein interaction sitesbase

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