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bose

Bioinformatics Centre
A.J.C. Bose Centenary Building,
P-1/12, CIT Scheme - VII M,
Kolkata - 700 054, India



Dr. PINAK CHAKRABARTI




RESEARCH I LAB MEMBERS I PUBLICATIONS

Senior Professor & Head

Centre of Excellence in Bionformatics

pinak@boseinst.ernet.in

pinak_chak@yahoo.co.in
Tel: +91-33-2569 3253

Fax:+91-33-2355 3886

[BIC Profile]

 

 

 

Area of Research:
Understanding of the structure and folding of proteins and their interactions with other molecules, large and small, using biophysical techniques (especially, X-ray crystallography) and database analysis

Key Publications:

Sonavane S, Chakrabarti P. Prediction of active site cleft using support vector machines. J Chem Inform Modeling (in press).


Dey S, Pal A, Chakrabarti P, Janin J. The subunit interfaces of weakly associated homodimeric proteins. J Mol Biol 2010; 398(1):146-160.


Chakraborti S, Chatterjee T, Joshi P, Poddar A, Bhattacharyya B, Singh SP, Gupta V, Chakrabarti P. Structure and activity of lysozyme on binding to ZnO nanoparticles. Langmuir 2010; 26(5):3506-3513.


Joshi P, Chakraborti S, Chakrabarti P, Haranath D, Shanker V, Ansari ZA, Singh SP, Gupta V. Role of surface adsorbed anionic species in antibacterial activity of ZnO quantum dots against Escherichia coli. J Nanosci Nanotechnol 2009;9(11):6427-6433.


Mukherjee D, Saha RP, Chakrabarti P. Structural and unfolding features of HlyT, a tetrameric LysR type transcription regulator of Vibrio cholerae. Biochim Biophys Acta 2009;1794(8):1134-1141.


Guharoy M, Chakrabarti P. Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes. J Comput Aided Mol Des 2009;23(9):645-654.


Bahadur RP, Chakrabarti P. Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins. BMC Struct Biol 2009;9.


Janin J, Bahadur RP, Chakrabarti P. Protein-protein interaction and quaternary structure. Q Rev Biophys 2008;41(2):133-180.


Sonavane S, Chakrabarti P. Cavities and Atomic Packing in Protein Structures and Interfaces. PLoS Computat Biol 2008;4(9): e1000188.

 

Chakrabarti P, Bhattacharyya R. Geometry of nonbonded interactions involving planar groups in proteins. Prog Biophys Mol Biol 2007;95:83-137.


Guharoy M, Chakrabarti P. Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein-protein interactions. Bioinformatics 2007;23:1909-1918.


Dasgupta B, Chakrabarti P, Basu G. Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif. FEBS Letters 2007;581:4529-4532.


Saha RP, Bahadur RP, Pal A, Mandal S, Chakrabarti P. ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces. BMC Struct Biol 2006;6:11.


Rodier F, Bahadur RP, Chakrabarti P, Janin J. Hydration of protein-protein interfaces. Proteins Struct Funct Bioinformatics 2005;60(1):36-45.


Guharoy M, Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci USA 2005;102:15447-15452.


Datta AB Panjikar S, Weiss MS, Chakrabarti P, Parrack P. Structure of λ CII: Implications for recognition of direct-repeat DNA by an unusual tetrameric organization. Proc Natl Acad Sci USA 2005;102:11242-11247.

 

Bahadur RP, Chakrabarti P, Rodier F, Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 2004;336(4):943-955.


Bhattacharyya R, Pal D, Chakrabarti P. Disulfide bonds, their stereospecific environment and conservation in protein structures. Protein Eng Design Selection 2004;17(11):795-808.


Pal L, Chakrabarti P, Basu G. Sequence and structure patterns in proteins from an analysis of the shortest helices: Implications for helix nucleation. J Mol Biol 2003;326(1):273-291.


Bahadur RP, Chakrabarti P, Rodier F, Janin J. Dissecting subunit interfaces in homodimeric proteins. Proteins Struct Funct Genetics 2003;53(3):708-719.


Bhattacharyya R, Chakrabarti P. Stereospecific interactions of proline residues in protein structures and complexes. J Mol Biol 2003;331(4):925-940.


Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins Struct Funct Genetics 2002;47(3):334-343.


Pal L, Basu G, Chakrabarti P. Variants of 310-helices in proteins. Proteins 2002;48:571-579.


Chakrabarti P, Pal D. The interrelationships of side-chain and main-chain conformations in proteins. Prog Biophys Mol Biol 2001;76:1-102.


Chakrabarti P, Pal D. Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations. J Mol Biol 1999;294:271-288.


Chakrabarti P, Chakrabarti S. C-H....O hydrogen bond involving proline residues in
α-helices. J Mol Biol 1998;284:867-873.


Chakrabarti P, Samanta U. CH/
π interaction in the packing of the adenine ring in protein structures. J Mol Biol 1995;251:9-14.


Chakrabarti P. Anion binding sites in protein structures. J Mol Biol;234:463-482.


Chakrabarti P. Systematics in the interaction of metal ions with the main-chain carbonyl group in protein structures. Biochemistry 1990;29:651-658.


Chakrabarti P. Geometry of interaction of metal ions with sulfur-containing ligands in protein strcutures. Biochemistry 1989;28:6081-6085
 




© Bioinformatics Centre (BIC), Bose Institute, Kolkata 2011, Last updated on: January 30, 2011