Debjani Roy

Assistant Professor
Ph.D.,(Computational Biology) New York University (USA)

 Contact information

 Telephone : +91-33-2569-3213          

E-mail : debjani@bic.boseinst.ernet.in,

              drdebjani@yahoo.com

Research interest  

We utilize computational methods to understand biological processes.  The aim of our studies is to unravel and explain biological phenomena in molecular and atomic detail using advanced computational and analytical approaches. 

The following are my current topics of research: 

Genome analysis 

  • Use of genomic information in understanding human diseases and in the identification of new molecular targets for drug discovery.
  • Study gene expression patterns of microbial pathogens.
  • Genome wide identification of cis-regulatory elements underlying gene co-regulation.

Computational structural biology 

  • Molecular modeling approaches for predicting molecular structures and interactions.
  • Structure based and ligand based pharmacophore modeling.
  • Virtual library design and screening.
  • Computational drug design.
  • Molecular dynamics simulations.

Analysis of gene expression microarray data and study biological networks:

  • Gene co-expression network analysis.
  • Integrating high throughput gene expression data from multiple sources to identify new network biomarkers for human diseases.

Publications:

  1. Kundu S and Roy D. (2012) Structural Analysis of Ca++ Dependent and Ca++ Independent Type II Antifreeze Proteins: A Comparative Molecular Dynamics Simulation Study. J Mol Graph Model. (In Press).

  2. Bandyopadhyay B, Das Gupta T, Roy D, Das Gupta SK. (2012) DnaK Dependence of the Mycobacterial Stress-Responsive Regulator HspR is Mediated through its Hydrophobic C-Terminal Tail. J Bacteriol. 194:4688-4697.

  3. Kundu S and Roy D. (2010) Structural study of carboxylesterase from hyperthermophilic bacteria Geobacillus stearothermophilus by molecular dynamics simulation. J Mol Graph Model. 28:820-827.

  4. Kundu S and Roy D. (2010) Structural study of biologically significant ligands with major birch pollen allergen Betv1 by docking and molecular dynamics simulation. Bioinformation, 4:326-330.  

  5. Banerjee R and Roy D. .(2009) Codon usage and gene expression pattern of Stenotrophomonas maltophilia R551-3 for pathogenic mode of living. Biochem Biophys Res Commun 390:177-181. 

  6. Kundu S and Roy D. (2009) Comparative structural studies of psychrophilic and mesophilic protein homologues by molecular dynamics simulation. J Mol Graph Model. 27:871-880. 

  7. Kundu S and Roy D. (2008) Temperature-induced unfolding pathway of a type III antifreeze protein: Insight from molecular dynamics simulation. J Mol Graph Model. 27:88-94.

  8. Kundu S and Roy D. (2007) Structural considerations for designing adenosine analogs as selective inhibitors of Trichomonas sp. glyceraldehyde-3- phosphate dehydrogenase. In Silico Biol. 7: 583-593.

  9. Kundu S and Roy D. (2007) Computational study of glyceraldehyde-3-phosphate dehydrogenase of Entamoeba histolytica: Implications for structure based drug design. J Biomol Struct Dyn. 25: 25-33. (Cover illustration). 

  10. Banerjee M, Roy D, Bhattacharya B, Basu G. (2007) Differential colchicine-binding across eukaryotic families: the role of highly conserved Pro268beta and Ala248beta residues in animal tubulin. FEBS Lett. 581: 5019-5023. 

  11. Roy D and Sengupta S. (2007) Structural Features of a cold-adapted Alaskan bacterial Lipase. J Biomol Struct Dyn  24: 463-470. (Cover illustration). 

  12. Chattopadhyay S, Sinha NK, Banerjee S, Roy D, Chattopadhyay D, Roy S. (2006) Small cationic protein from a marine turtle has beta-defensin-like fold and antibacterial and antiviral activity. Proteins  64: 524-531. 

  13. Ghosh Dastidar K, Maitra S, Goswami L, Roy D, Das KP, Majumder AL. (2006) An insight into the molecular basis of salt tolerance of L-myo-inositol 1-P synthase (PcINO1) from Porteresia coarctata (Roxb.) Tateoka, a halophytic wild rice. Plant Physiol. 140: 1279-1296.  

  14. Gupta S, Banerjee M, Poddar A, Banerjee A, Basu G, Roy D and Bhattacharya B. (2005) The biphasic kinetics of Colchicine-Tubulin interaction: Role of amino acids surrounding the A-ring of bound colchicine molecule. Biochemistry  44: 10181-10188. 

  15. Bagchi A, Roy D, Roy P. (2005) Homology modeling of a transcriptional regulator SoxR of the lithotrophic sulfur oxidation (Sox) operon in α-Proteobacteria. J Biomol Struct Dyn 22: 571-577. 

  16. Roy D and Lohia A. (2004) Sequence divergence of Entamoeba histolytica tubulin is responsible for its altered tertiary structure. Biochem Biophys Res Commun 319:1010-1016. 

  17. Banerjee S, Hess D, Majumder P, Roy D, Das S. (2004) The interactions of allium sativum leaf agglutinin with a chaperonin group of unique receptor protein isolated from a bacterial endosymbiont of the mustard aphid. J Biol Chem. 279: 23782-23789.  

  18. Roy D, Ghosh D, Gupta-Bhattacharya S. (2003) Homology modeling of allergenic cyclophilins: IgE-binding site and structural basis of cross-reactivity. Biochem Biophys Res Commun. 307:422-429. 

  19. Roy D, Mukhopadhyay C. (2002) Molecular dynamics simulation of GM1 in phospholipid bilayer. J Biomol Struct Dyn. 19: 1121-1132. 

  20. Ghose M, Mandal S, Roy D, Mandal R K, Basu G. (2001) Dielectric relaxation in a single tryptophan protein. FEBS Lett. 509: 337-340. 

  21. Roy D, Mukhopadhyay C. (2001) GD1a in phospholipid bilayer: A molecular dynamics simulation. J Biomol Struct Dyn. 18: 639-646. 

  22. Roy D, Hingerty B E, Shapiro R and Broyde S. (1998) Stabilization of Slipped Mutagenic Intermediates in the NarI mutational hotspot sequence: AF and AAF modified guanines in the syn conformation stabilize the slipped form. Chem Res Toxicol 11: 1301-1311. 

  23. Roy D, Hingerty B E, Shapiro R and Broyde S. (1997) Modeling DNA Replication Intermediates. Structure, Motion, Interaction and Expression of Biological Macromolecules. Proceedings of the tenth conversation. State University of New York, Albany, NY  267-277. 

  24. Lo P.C. H. Roy D, Mount S M. (1994) Supressor U1snRNAs In Drosophila. Genetics 138: 1-14. 

  25. Kurkolos M, Weinberg J M, Roy D and Mount S M. (1993) P Element-mediated in Vivo Deletion analysis of white-apricot: Deletions between direct repeats are strongly favored. Genetics 136: 1001-1011.