Pinak Chakrabarti
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Recent Submissions
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ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces
(BIOMED CENTRA, 2006-06-07)Molecular recognition is all pervasive in biology. Protein molecules are involved in enzyme regulation, immune response, signal transduction, oligomer assembly, etc. Delineation of physical and chemical features of the ... -
Domain analysis of a groundnut calcium-dependent protein kinase - Nuclear localization sequence in the junction domain is coupled with nonconsensus calcium binding domains
(AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY, 2006-04-14)The signature of calcium-dependent protein kinases (CDPKs) is a C-terminal calmodulin-like domain (CaMLD) with four consensus calcium-binding sites. A junction domain (JD) joins the kinase with CaMLD and interacts with ... -
3(10)-Helix Adjoining a -Helix and b -Strand: Sequence and Structural Features and Their Conservation
(WILEY-BLACKWELL, 2005-06-15)Does the amino acid use at the terminal positions of an a-helix become altered depending on the context-more specifically. when there is an adjoining 3(10)-helix, and can a single helical cylinder encompass the resultant ... -
Conservation and relative importance of residues across protein-protein interfaces
(NATL ACAD SCIENCES, 2005-10-25)A core region surrounded by a rim characterizes biological interfaces. We ascertain the importance of the core by showing the sequence entropies of the residues comprising the core to be smaller than those in the rim. Such ... -
Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU
(BIOMED CENTRAL, 2006-11-20)Background: The SmtB/ArsR family of prokaryotic metal-regulatory transcriptional repressors represses the expression of operons linked to stress-inducing concentrations of heavy metal ions, while derepression results from ... -
Structural studies on Vibrio cholerae ToxR periplasmic and cytoplasmic domains
(ELSEVIER, 2007-10)The transcription activator ToxR controls the expression of cholera toxin, pilus colonization factor and outer membrane protein in Vibrio cholerae. It binds to the 5'-TTTTGAT-3' tandernly repeated DNA sequence in the cholera ... -
Prediction of Active Site Cleft Using Support Vector Machines
(AMER CHEMICAL SOC, 2010-12)Computational tools are available today for the detection and delineation of the clefts and cavities in protein 3D structure and ranking them on the basis of probable binding site clefts. There is a need to improve the ... -
Conserved residue clusters at protein-protein interfaces and their use in binding site identification
(BIOMED CENTRAL, 2010-05-27)Background: Biological evolution conserves protein residues that are important for structure and function. Both protein stability and function often require a certain degree of structural co-operativity between spatially ... -
The Subunit Interfaces of Weakly Associated Homodimeric Proteins
(ACADEMIC PRESS, 2010-04-23)We analyzed subunit interfaces in 315 homodimers with an X-ray structure in the Protein Data Bank, validated by checking the literature for data that indicate that the proteins are dimeric in solution and that, in the case ...
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