LMPID: A manually curated database of linear motifs mediating protein–protein interactions

Linear motifs (LMs), used by a subset of all protein–protein interactions (PPIs), bind to globular receptors or domains and play an important role in signaling networks. LMPID (Linear Motif mediated Protein Interaction Database) is a manually curated database which provides comprehensive experimentally validated information about the LMs mediating PPIs from all organisms on a single platform. About 2200 entries have been compiled by detailed manual curation of PubMed abstracts, of which about 1000 LM entries were being annotated for the first time, as compared with the Eukaryotic LM resource. The users can submit their query through a user-friendly search page and browse the data in the alphabetical order of the bait gene names and according to the domains interacting with the LM. LMPID is freely accessible at http://bicresources.jcbose. ac.in/ssaha4/lmpid and contains 1750 unique LM instances found within 1181 baits interacting with 552 prey proteins. In summary, LMPID is an attempt to enrich the existing repertoire of resources available for studying the LMs implicated in PPIs and may help in understanding the patterns of LMs binding to a specific domain and develop prediction model to identify novel LMs specific to a domain and further able to predict inhibitors/modulators of PPI of interest. Database URL: http://bicresources.jcbose.ac.in/ssaha4/lmpid

[1]  Jerome Wielens,et al.  Oncogenic protein interfaces: small molecules, big challenges , 2014, Nature Reviews Cancer.

[2]  Increasing the range of drug targets , 2012, Bioengineered.

[3]  Victor Neduva,et al.  Peptides mediating interaction networks: new leads at last. , 2006, Current opinion in biotechnology.

[4]  Jonathan G. Lees,et al.  Transient protein-protein interactions: structural, functional, and network properties. , 2010, Structure.

[5]  R. Russell,et al.  Peptide-mediated interactions in biological systems: new discoveries and applications. , 2008, Current opinion in biotechnology.

[6]  Bruce Randall Donald,et al.  Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity , 2012, PLoS Comput. Biol..

[7]  Sanguthevar Rajasekaran,et al.  Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences , 2011, Nucleic Acids Res..

[8]  Ignacio E. Sánchez,et al.  The eukaryotic linear motif resource ELM: 10 years and counting , 2013, Nucleic Acids Res..

[9]  Michael B. Yaffe,et al.  Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs , 2003, Nucleic Acids Res..

[10]  Lucy Skrabanek,et al.  PDZBase: a protein?Cprotein interaction database for PDZ-domains , 2005, Bioinform..

[11]  Jyoti Rani,et al.  pubmed.mineR: An R package with text-mining algorithms to analyse PubMed abstracts , 2015, Journal of Biosciences.

[12]  Ulrik Schulze,et al.  Can emerging drug classes improve R&D productivity? , 2013, Drug discovery today.

[13]  M. Sánchez-Niño,et al.  TWEAKing renal injury. , 2008, Frontiers in bioscience : a journal and virtual library.

[14]  Niall J. Haslam,et al.  Understanding eukaryotic linear motifs and their role in cell signaling and regulation. , 2008, Frontiers in bioscience : a journal and virtual library.

[15]  Olivier Sperandio,et al.  iPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions. , 2013, Drug discovery today.

[16]  Sanguk Kim,et al.  Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks , 2014, PLoS Comput. Biol..