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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
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