Structural Biology & Bio-Informatics Division

Dr. Saikat Chakrabarti

Principal Scientist
Ramalingaswami Fellow

Contact: saikat@iicb.res.in / saikat273@gmail.com
Phone: +91-033-24995809

Previous Positions

Staff Scientist @ NCBI/NLM/NIH, 2009
Postdoctoral Fellow @ NCBI/NLM/NIH, 2004-2009
PhD @ NCBS, TIFR, Bangalore, India, 1999-2004

Lab Website: http://www.hpppi.iicb.res.in/saikatlab/

Current Research Interest

We are a Bioinformatics and Computational Biology group. Our current research interests are to study protein structure, function, evolution and networks that are crucial for host pathogen interactions. Our primary emphasis is towards understanding the different modalities and specificities of host-pathogen protein-protein interactions (PPI).

Though PPI databases are available yet more information is still buried under unstructured data present in literature. Hence, our lab is interested in developing better text mining tools which enables extraction of meaningful information from text and databases and provides novel relations between various biomedical entities.

Construction and analysis of PPI network is done from two perspectives - biological and topological. From network analysis we predict important pathogen proteins which are crucial for its own sustenance and for infecting the host. Similarly, by developing effective in silico knock out models of target proteins we show their global and local impact in PPI network. Along with these network analyses we are also interested in molecular modeling, docking and molecular simulation studies to explore the interactions in molecular details.

In short, our aim is to undertake a multi-faceted research plan integrating the available experimental information with subsequent development and application of several computational techniques for better understanding and prediction of molecular mechanisms underlying specific host-pathogen interactions.

 

Names of the group members including regular staff with designation and research fellows

Fellows / RA

  1. Abhijit Chakraborty (SRF) [email: avijit.novus@gmail.com]
  2. Anindyajit Banerjee (SPF) [email: anindyajit@gmail.com]
  3. Sapan Mandloi (SRF) [email: sapan.bioinfo@gmail.com]
  4. Madhumita Bhattacharyya (SRF) [email: madhu84.life@gmail.com]
  5. Aneesha Das (SRF) [email: dasaneesha@gmail.com]
  6. Shreemoyee Dutta Majumder (JRF) [email: shreemoyeeduttamajumder@gmail.com]
  7. Arghya Adhya (PF) [email: arghyaadhya@gmail.com]
  8. Tanmayee Rath(PF) [email: tanmayeerath3@gmail.com]
  9. Ishita Mukherjee(JRF) [email: mukishi@gmail.com]
  10. Harshita Tiwari(Trainee) [email: harshita.tewari@gmail.com]

Positions Available

Students who are enthusiastic, motivated and passionate to explore multi-disciplinary scientific research field should get in touch directly with Dr. Saikat Chakrabarti at saikat273@gmail.com, saikat@iicb.res.in. PhD candidates should pass CSIR/UGC/ICMR NET JRF Fellowship Exam. Students who are willing to work as temporary project fellow under certain projects should get in touch at saikat273@gmail.com, saikat@iicb.res.in and also should look suitable positions at www.career.iicb.res.in

List of Publications and Book Chapters

  1. Paul A, Samaddar S, Bhattacharya A, Banerjee A, Das A, Chakrabarti S, DasGupta M. (2014) Gatekeeper tyrosine phosphorylation is autoinhibitory for Symbiosis Receptor Kinase. Imapct factor: 3.470.
  2. Anshu, A., Mannan, A., Chakraborty, A., Chakrabarti, S., Dey, M.(2014) A Novel Role for Protein Kinase Kin2 in Regulating HAC1 mRNA Translocation,Splicing and Translation. Mol Cell Biol.
  3. Banerjee, A., Dey, S., Chakraborty, A., Datta, A., Basu, A.,Chakrabarti, S. and Datta, S. (2014) Binding mode analysis of a major T3SS translocator protein PopB with its chaperone PcrH from Pseudomonas aeruginosa. Proteins (inpress). Imapact factor: 2.921
  4. Nayak, M.K., Agrawal, A.S., Bose, S., Naskar, S., Bhowmick, R.,Chakrabarti, S., Sarkar, S. and Chawla-Sarkar, M. (2014) Antiviral activity of baicalin against influenza virus H1N1-pdm09 is due to modulation of NS1-mediated cellular innate immune responses. J Antimicrob Chemother, 69, 1298-1310. Impact factor: 4.686
  5. Chakraborty, A., Mukherjee, S., Chattopadhyay, R., Roy, S. and Chakrabarti, S. (2014) Conformational Adaptation in the E. coli Sigma 32 Protein in Response to Heat Shock. J Phys Chem B, 118, 4793-4802.
    Impact factor: 3.607
  6. Chakraborty, A. and Chakrabarti, S. (2014) A survey on prediction of specificity-determining sites in proteins. Brief Bioinform. Impact factor: 5.298
  7. Roy, K., Ghosh, M., Pal, T.K., Chakrabarti, S. and Roy, S. (2013) Cholesterol lowering drug may influence cellular immune response by altering MHC II function. J Lipid Res, 54, 3106-3115. Impact factor: 5.559
  8. Mazumder, A., Bose, M., Chakraborty, A., Chakrabarti, S. and Bhattacharyya, S.N. (2013) A transient reversal of miRNA-mediated repression controls macrophage activation. EMBO Rep, 14, 1008-1016. Impact factor: 7.189
  9. Debashree De, Piyali Datta Chakraborty, Jyotirmoy Mitra, Kanika Sharma, Somnath Mandal, Aneesha Das, Saikat Chakrabarti and Debasish Bhattacharyya(2013). Ubiquitin-like Protein from Human Placental Extract has Collagenase Activity. PLoS ONE  8(3) : e59585. Impact factor:4.092 (2011).
  10. Goyal, Manish; Alam, Athar; Iqbal, Mohd; Dey, Sumanta; Bindu, Samik; Pal, Chinmay; Banerjee, Anindyajit; Chakrabarti, Saikat; Bandyopadhyay, Uday (2011). Identification and molecular characterization of an Alba-family protein from human malaria parasite Plasmodium falciparum. Nucleic Acid Res 40, 1174-90. Impact factor: 7.836 (2010).
  11. Chakraborty,  Abhijit; Ghosh, Sudeshna; Chowdhary, Garisha; Maulik,Ujjwal; Chakrabarti, Saikat* (2012). DBETH: A Database of Bacterial Exotoxins for Human. Nucleic Acid Res 40, D615-20. Impact factor: 7.836(2010).
  12. Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher; Panchenko, Anna; Chakrabarti, Saikat* (2012). SPEER-SERVER: A web server for prediction of protein specificity determining sites. Nucleic Acid Res 40, W242-248. Impact factor: 7.836 (2012).
  13. Saikat Chakrabarti* and Anna R. Panchenko*. (2010). Structural and functional roles of coevolved sites in proteins. PLoS ONE. 5(1):e8591. Impact factor: 4.351 (2009).
  14. Ganesan Pugalenthi, Tank K, P.N. Suganthan, Christopher J. Lanczycki and Saikat Chakrabarti*. (2009).Prediction of functionally important sites of proteins using neural network ensemble approach. Biochem Biophys Res Commun. 384, 155-159. Impact factor: 2.82 (2006).
  15. Saikat Chakrabarti* and Anna Panchenko. (2009). Ensemble approach to predict specificity determinants: benchmarking and validation. BMC Bioinformatics 10, 207. Impact factor: 3.62 (2006).
  16. Ganesan Pugalenthi, Tank K, P.N. Suganthan and Saikat Chakrabarti*. (2009). Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. Bioinformatics, Nov 27 (Epub ahead of print). Impact factor: 4.894 (2006).
  17. Saikat Chakrabarti* and Anna R. Panchenko*. (2009). Coevolution in defining the functional specificity.Proteins, 75, 231-240. Impact factor: 4.684 (2006).
  18. Christopher J. Lanczycki and Saikat Chakrabarti* (2008). A tool for the prediction of functionally important sites in proteins using a library of functional templates. Bioinformation, 2, 279-283. Impact factor: NA.
  19. Ganeshan Pugalenthi, P.N. Suganthan, R. Sowdhamini and Saikat Chakrabarti*. (2008). MegaMotifBase: a database of structural motifs in protein families and superfamilies. Nucleic Acids Research. 36 (database issue).Impact factor: 6.317 (2006).
  20. Saikat Chakrabarti*, Stephen H. Bryant and Anna R. Panchenko (2007). Functional specificity lies within the properties and evolutionary changes of amino acids. J Mol Biol. 373(3):801-10. Impact factor: 4.890 (2006).
  21. Ganesan Pugalenthi, P.N. Suganthan, R. Sowdhamini and Saikat Chakrabarti*. (2007). SMotif: A server for structural motifs in proteins. Bioinformatic. 23, 637-638. Impact factor: 4.894 (2006).
  22. Saikat Chakrabarti* and Christopher J. Lanczycki. (2007). Analysis and Prediction of Functionally Important Sites in Proteins. Protein Science, 16, 4-13. Impact factor: 3.642 (2006).
  23. Saikat Chakrabarti*, Christopher J. Lanczycki, Anna R. Panchenko,Teresa M. Przytycka, Paul A. Thiessen and Stephen H. Bryant. (2006). State of the art: refinement of multiple sequence alignments. BMC Bioinformatics, 7, 499. Impact factor: 3.62 (2006).
  24. Chakrabarti, S., Manohari, G., Pugalenthi, G. and R. Sowdhamini. (2006). SSToSS - Sequence-Structural Templates of Single-member Superfamilies. In Silico Biology. 6, 0029. Impact factor: NA.
  25. Chakrabarti, S., Lanczycki, CJ., Panchenko, AR., Przytycka, TM., Thiessen, PA and Bryant SH. (2006). Refining multiple sequence alignments with conserved core regions. Nucleic Acid Res. 34, 2598-606. Impact factor: 6.317(2006).
  26. Bhadra R, Sandhya S, Abhinandan KR, Chakrabarti S, Sowdhamini R, Srinivasan N. (2006). Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. Nucleic Acids Res. 34:W143-6.Impact factor: 6.317 (2006).
  27. S. Sandhya, S. Chakrabarti, K.R. Abhinandan, R. Sowdhamini and N.Srinivasan. (2005). Detection of remote similarities between proteins by cascading PSI-BLAST. Journal of Biomolecular Structure and Dynamics. 23(3):283-98. Impact factor: 1.299 (2006).
  28. Chakrabarti, S., Prem, AA., Bhardwaj, N, and Sowdhamini R (2004). SCANMOT: search for protein homologues in sequence databases using simultaneous restraints of multiple motifs. Nucleic Acid Research, 33:W274-6. Impact factor: 6.317 (2006).
  29. Chakrabarti, S., Bhardwaj, N., Prem, AA, and Sowdhamini R. (2004) Improvement of Alignment Accuracy Utilizing Sequentially Conserved Motifs. BMC Bioinformatics, 5 (1):167. Impact factor: 3.62 (2006).
  30. Chakrabarti, S., Jaisurya, J., and Sowdhamini, R. (2004). Improvement of Comparative Modeling: application of spatial orientation of motifs as additional restraints. Journal of Molecular Modeling. 10, 69-75. Impact factor: 1.384 (2006).
  31. Chakrabarti, S, and Sowdhamini, R. (2003) Regions of minimal structural variation among members of protein domain superfamilies: Application to remote homology detection and modeling using distant relationships.  FEBS Letters. 569, 31-6. Impact factor: 3.372 (2006).
  32. Chakrabarti, S., Venkataramanan, K., and Sowdhamini, R. (2003) SMoS: A database of Structural Motifs of Superfamily. Protein Eng. 2003 Nov; 16, 791-3. Impact factor: 3.0 (2006).
  33. Chakrabarti, S and Sowdhamini, R (2003) Functional sites and evolutionary connections of Acyl Homoserine Lactone synthases. Protein Eng. 16, 271-278. Impact factor: 3.0 (2006).

*Author for correspondence.

Book Chapters

  1. Chakrabarti,S., Bhavana, S., Mallika, V., and Sowdhamini, R. (2002) Protein Structural Similarities and Prediction of Protein Function. RecentTrendsinChemistry. Ed. Srivastava, M.M. India.
  2. Chakrabarti,S and Sowdhamini, R. (2006) Potentials of fold recognition methods in structure prediction of homoserine lactone synthases. TrendsinBioinformatics. Ed. P. Shanmughavel, MKU, Madurai.
  3. S. Sandhya, C. Jayadev, K.R. Abhinandan, S.Chakrabarti, R.  Sowdhamini and N. Srinivasan (2005) Relating Protein Families in Sequence Space through Multiple Intermediates. Mathematical Biology: Recent Trends. Eds. Peeyush Chandra and B. V. Rathish Kumar, New Delhi. India.

Web Publications

  1. Chakrabarti, S., Venkataramanan, K., and Sowdhamini, R. (2003) Enhancement of PASS2 database by the Inclusion of Structural Motifs of Aligned Protein Domain Superfamilies. Nucleic Acids Res., http://www3.oup.co.uk/nar/database/summary/275.
  2. Chakrabarti, S., Manohari, G., and Sowdhamini, R. (2003) SSToSS: A database of Sequence-Structural Templates of Single member Superfamilies. Nucleic Acids Res., http://www3.oup.co.uk/nar/database/summary/530.
 
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