Functional Interactomics Lab

Bioinformatics Center, Bose Institute

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Databases/Web-servers

News / Updates

Ph.D postions are available for individuals with wet-lab experience and CSIR/ICMR-NET JRF for functional interactomics and proteomics work.
One project JRF postion is available (M.Sc/M.Tech/MCA).
Two joint projects approved from ICMR in 2014-2017.

Databases

Ring-Hydroxylating Oxygenase database(RHOBASE) :

The Ring-Hydroxylating Oxygenase database, abbreviated as “RHObase”, is a web based, manually curated and searchable database which provides comprehensive information on all biochemically studied and characterized bacterial Rieske-type RHOs. Environ Microbiol Rep. 2014 Oct;6(5):519-23.
PMID: 25646545

Linear Motif mediated Protein Protein Interaction Database (LMPID) :

LMPID is a publicly available web-based relational database of experimentally verified linear motif instances mediating Protein-Protein Interactions (PPIs) from all organisms, compiled by manual curation of existing literature. Database (Oxford). 2015. PMID: 25776024

Database of Allergy and Asthma Biomarkers (DAAB) :

DAAB is an online database of Allergy And Asthma Biomarkers compiled by manual curation of literature.Clin Exp Allergy .2015. doi: 10.1111/cea.12569. PMID: 25973645

MYCbase: A Database of MYC

MYCbase is a manually-curated and web-based repository that provides comprehensive information on myc gene mutations, documented from various publications
BMC Bioinformatics, 2017 Apr 28;18(1):224. PMID: 28454513

PPIMdb: database of small molecules that inhibit orthosteric Protein-Protein Interactions (PPIs)

This database contains both experimentally verified and predicted compounds for three popular PPI complexes Such as, Mdm2/P53, Bcl2/Bak and c-Myc/Max.

PSCRIdb: A database of regulatory interactions in Pluripotent Stem Cells

PSCRIdb, a manually curated database composed of protein-protein, protein-DNA, gene-gene and miRNA-mRNA interaction datasets in human and mouse pluripotent stem cells(PSCs).

DRAGdb: Drug Resistance Associated Genes

DRAGdb, a manually curated database for mutational data across bacterial pathogenic strains with reference to DRAGs reported in Mycobacterium tuberculosis.

Web-servers

Linear Motif Domain Interaction Prediction (LMDIPred) :

LMDIPred is a web server that predicts the occurrence of linear motifs that may mediate interactions with SH3, WW and PDZ domains, within a user-provided amino-acid sequence.

Prediction of Protein Protein Interaction in Enteropathogen (EnPPIpred) :

EnPPIpred is a prediction server that predicts Protein-Protein Interactions (PPIs) in entheropathogens including E.coli, Vibrio cholerae, Salmonella Typhi, Shigella & Yersinia. The E.coli data set was used to build the SVM Classifier model.

Citations: Barman RK, Jana T, Das S, Saha S* Prediction of Intra-species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study PLoS One. 2015 Dec 30;10(12):e0145648 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145648
PMID: 26717407

Prediction of Protein Protein Interaction Modulators (PPIMpred) :

PPIMpred is a prediction server of small molecules that inhibit Protein-Protein Interactions (PPIs).
Citations: Jana T, Ghosh A, Das Mandal S, Banerjee R, Saha S. 2017 PPIMpred:a web server for high-throughput screening of small molecules targeting protein–protein interaction.R. Soc. open sci.4: 160501. http://dx.doi.org/10.1098/rsos.1605 PMID: 28484602

Prediction of puripotent responsible proteins (PluriPred) :

Pluripred is a web server for prediction of the proteins which have important role in pluripotency.
J Biosci. 2016 Dec;41(4):743-750. PMID: 27966493

Support vector Machine (SVM) based prediction of therapeutic activity of Protein-Protein Interaction Modulators in-terms of half maximal inhibitory concentration (IC50) (PPIM-IC50Pred) :

SVM regression based webserver to predict the IC50 values (nM) of small molecules PPIMs as the therapeutic activity.