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Structural Biology & Bio-Informatics Division

Dr. Saikat Chakrabarti

Scientist
Ramalingaswami Fellow, 2009-10.

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

Contact:
E-mail: saikat@iicb.res.in; saikat273@gmail.com;
Phone: +91-033-24995809
Other homepage: http://www.ncbi.nlm.nih.gov/CBBresearch/Fellows/Chakrabarti/

 

Current Research Interest

  • Our current research interests are to study the structure, function and evolution of the proteins that are crucial for several kinds of pathogen mediated disorders. Our primary emphasis would be towards understanding the different modalities and specificities of host-pathogen protein-protein interactions (PPI). Not many systematic methods have been reported for predicting physical and/or functional interactions between host and pathogen proteins. Computational prediction of such interactions is an important unsolved problem. Therefore, development of new computation techniques that integrate various modes experimental information for a better understanding in host-pathogen interaction mechanism is due. Identification and prediction of possible novel modes and partners in host-pathogen PPIs is also very important.

    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.

Positions Available:

Positions will be open for individuals with NET (CSIR/UGC) fellowships to conduct research. Interested candidate may contact directly at saikat273@gmail.com or saikat@iicb.res.in.

List of important Publications:

Book Chapters:

  1. Chakrabarti, S., Bhavana, S., Mallika, V., and Sowdhamini, R. (2002) Protein Structural Similarities and Prediction of Protein Function. Recent Trends in Chemistry. Ed. Srivastava, M.M. India.
  2. Chakrabarti, S and Sowdhamini, R. (2006) Potentials of fold recognition methods in structure prediction of homoserine lactone synthases. Trends in Bioinformatics. 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.

Reserch Articles:

  1. 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).
  2. 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).
  3. 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).
  4. 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).
  5. 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).
  6. 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).
  7. 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).
  8. 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).
  9. 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).
  10. 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.
  11. 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).
  12. 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).
  13. 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).
  14. Ganesan Pugalenthi, P.N. Suganthan, R. Sowdhamini and Saikat Chakrabarti*.(2007). SMotif: A server for structural motifs in proteins. Bioinformatics., 23, 637-638. Impact factor: 4.894 (2006).
  15. 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).
  16. 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.
  17. Saikat Chakrabarti* and Anna R. Panchenko*. (2009). Coevolution in defining the functional specificity. Proteins 75, 231-240. Impact factor: 4.684 (2006).
  18. 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 Impact factor: 4.894 (2006).
  19.  Saikat Chakrabarti* and Anna Panchenko. (2009). Ensemble approach to predict specificity determinants: benchmarking and validation. BMC Bioinformatics 10, 207. Impact factor: 3.62 (2006).
  20. 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)
  21. Saikat Chakrabarti* and Anna R. Panchenko*. (2009). Structural and functional roles of coevolved sites in proteins. (in press) PLoS ONE.
  22. Saikat Chakrabarti* and Anna R. Panchenko*. (2009). A survey of prediction of specificity determining sites: advances and pitfalls. (Review; in preparation).

*Author for correspondence.

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Updated on 21.12.2009