Research Groups
Mammalian Biology: Structural and Computational Biology
Research Interests and Description
Staff Research Scientist: Dinesh Gupta
Group Leader: Amit Sharma
Group Members
Research Interests
Computational Biology, cyclins, virulent proteins, molecular modelling, in-silico screening, miRNA.Description of Research
Computational biology studies
The scientific interests of Dr. Gupta's group
include use of computational biology tools to solve research problems in the
post genomic era. The Group has developed several protein sequence databases
including- ProtRepeatsDB: a database of different types of protein repeats
sequences in genomes (http://bioinfo.icgeb.res.in/repeats), ProtvirDB: a
database of protozoan virulent protein sequences
(http://bioinfo.icgeb.res.in/protvirdb). This group has also developed
several artificial intelligence based web servers for methods to solve
bioinformatics problems such as prediction of cyclin sequences virulence proteins
and lipocalins. Other research interests of the group include comparative
genomics to identify regulatory elements like miRNAs and transcription factors
in genomes. Dr. Gupta's group collaborates with malaria group for validation of their
prediction methods for Plasmodium proteins. CyclinPred has been used to identify
cyclins in Plasmodium genomes; few of the putative predicted cyclins have been
cloned and expressed; the CDK partners of the cyclins are being explored. Based
on large scale molecular modeling of Plasmodium falciparum proteins, and its comparisons
with host proteins, an ortholog of prokaryotic hslV, a parasite specific
protease in Plasmodium falciparum (PfHslV) has been identified as a new drug
target. Currently, the Group has identified inhibitors against the protein
using in silico techniques, which are being validated experimentally.
Recent Publications
Kalita, M.K., Nandal, U.K., Pattnaik, A., Sivalingam, A., Ramasamy, G., Kumar, M., Raghava, G.P., Gupta, D. 2008. CyclinPred: a SVM-based method for predicting cyclin protein sequences. PLoS ONE, 3, e2605Garg, A., Gupta, D. 2008. VirulentPre: a SVM based prediction method for virulent proteins in bacterial pathogens. BMC Bioinformatics 9, 62
Subramaniam, S., Mehrotra, M, Gupta, D. 2008. Virtual high throughput screening (vHTS) - A perspective. Bioinformation 3, 14
Ramasamy, G., Gupta, D., Mohmmed, A., Chauhan, V.S. 2007. Characterization and localization of Plasmodium falciparum homolog of prokaryotic ClpQ/HslV protease. 2007. Mol. Biochem. Parasitol. 152, 139-148
Kalita, M.K., Ramasamy, G., Duraisamy, S., Chauhan, V.S., Gupta, D. 2006. ProtRepeatsDB database of amino acid repeats in genome. BMC Bioinformatics 7, 336
Gowthaman, R., Duraisamy, S., Kalita, M.K., Gupta, D. 2005. A database for Plasmodium falciparum protein models. Bioinformation 1, 50
