PeptideMine - WebServer for Identification and analysis of peptides from interacting proteins :
PeptideMine is a webserver developed for identifying and analysing peptides suitable for protein-peptide binding studies. PeptideMine is using a unique, knowledge based approach for the identification of peptides from the interacting sequence-space of a protein using different search programs (PeptideMine Search, BLASTP and regular expression based pattern). The peptides identified using the searches can be examined using different peptide related features. User can perform specific searches using different search programs with in the interacting partners of a given gene. Integrated GO annotations, protein-protein interaction data, peptide-domain mapping, domain-domain interaction data and various peptide related feature calculation provides a reliable approach to identify new peptides for protein-peptide binding studies. Using PeptideMine user can select interesting peptides for in-vitro and in-silico studies. Current version of PeptideMine is available for 6 genomes.
PeptideMine - Methodology:
Integrated data mining approaches to extract biologically valid information from data biological data sources has become a reliable venture in post-genome bioinformatics. Applications of such integrated approaches are proved to be useful in different levels of function association and enhanced annotations of gene products. Such methods based on interaction data, functional features, Gene Ontology are useful to identify new connections that could be the starting point of new hypothesis in different domains of biology. PeptideMine is a webserver developed for experimental and computational biologists interested in identifying and analysing peptides suitable for protein-peptide binding studies. A large number of enzymes, like proteases, kinases and phosphatases, recognise peptides and proteins as their substrates. However, accurate information on substrates for these enzymes is not available due to paucity of experimental data. PeptideMine is using a unique, knowledge based approach for the identification of peptides from the interacting sequence-space of a protein using different search programs (PeptideMine Search, BLASTP and regular expression based pattern). The peptides identified using the searches can be examined using different peptide related features like molecular weight, pI, instability index, GRAVY, charge, amino acid composition and molar absorption coefficient. User can also generate amino acid index based plots using the peptides using 516 amino acid indices. Functional annotations of the interacting proteins are also provided using the organism specific GO annotations of the gene and each peptide is further scanned for potential PROSITE patterns. Secondary structure and disorder regions are also provided to support the interaction specificities of these peptides. To provide more clarity about the peptides as probable candidates for in-vitro or in-silico studies, we mapped the location of peptide to its domain and possible domain-domain interactions are assigned to the peptide-containing domains and its probable interacting domains in the query protein. The interacting proteins are obtained from STRING and domain-domain interaction data is obtained from DOMINE. Domain architectures are elucidated using the hmmpfam (HMMER) and domain-domain interactions are established using the reliable E-value cut-off and further assessment of the coverage. PeptideMine will be a useful resource for peptide-ligand identification from interacting partners, finding homologous peptides and patterns in interacting space of a protein, designing peptide arrays, generating peptide libraries and protein-peptide docking.
PeptideMine - References:
Von Mering, C. et. al. (2007) STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35:D358−D362.
Ashburner, M. et. al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25:25−29.
Raghavachari B. et. al. (2007). DOMINE: A database of protein domain interactions, Nucleic Acids Research, 36, D656-661, 2008.
Altschul, S. F. et. al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
McGuffin, L. J., et al. (2000) The PSIPRED protein structure prediction server. Bioinformatics 16:404-405.
Eddy, S. (1998) Profile hidden markov models. Bioinformatics, 14, 755–763.
Gasteiger E., et. al. (2005) Protein Identification and Analysis Tools on the ExPASy Server; (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press pp. 571-607.
Edouard de Castro et al. (2000) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 34:W362-W365.
Guruprasad, K., et. al. (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. 4,155-161.
Brown, N.P. et al. (1998) MView: A Web compatible database search or multiple alignment viewer. Bioinformatics 14:380-381.
Stajich JE, et.al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res, 12. 1611-1618.
Contact: Prof. R. Sowdhamini (Contact : mini@ncbs.res.in)
Prof. B. Gopal (Contact : bgopal@mbu.iisc.ernet.in)
PeptideMine - Team:
K. Shameer, LL Madan, S. Veeranna, Prof. B. Gopal & Prof. R. Sowdhamini
