Browsing Prof. Pinakpani Chakrabarti by Title
Now showing items 1-20 of 28
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310-Helix adjoining α-helix and β-strand: Sequence and structural features and their conservation
(WILEY-BLACKWELL, 2005-06-15)Does the amino acid use at the terminal positions of an α-helix become altered depending on the context-more specifically, when there is an adjoining 310-helix, and can a single helical cylinder encompass the resultant ... -
Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display
(BIOMED CENTRAL, 2009-04-08)Background: Depending on chemical features residues have preferred locations – interior or exterior – in protein structures, which also determine how many other residues are found around them. The close packing of residues ... -
BioSuite: A comprehensive bioinformatics software package (A unique industry-academia collaboration)
(CURRENT SCIENCE ASSN, 2007-01-10) -
Cavities and Atomic Packing in Protein Structures and Interfaces
(PUBLIC LIBRARY SCIENCE, 2008-09)A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules ... -
Cavities in protein–DNA and protein–RNA interfaces
(OXFORD UNIV PRESS, 2009-08)An analysis of cavities present in protein-DNA and protein-RNA complexes is presented. In terms of the number of cavities and their total volume, the interfaces formed in these complexes are akin to those in transient ... -
Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins
(BIOMED CENTRAL, 2009-12-28)Background: Setting the rules for the identification of a stable conformation of a protein is of utmost importance for the efficient generation of structures in computer simulation. For structure prediction, a considerable ... -
A Dissection of Specific and Non-specific Protein-Protein Interfaces
(ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2004-02-27)We compare the geometric and physical-chemical properties of interfaces involved in specific and non-specific protein-protein interactions in crystal structures reported in the Protein Data Bank. Specific interactions are ... -
Dissection, residue conservation, and structural classification of protein-DNA interfaces
(WILEY-LISS, 2009-02-15)The basic DNA-binding modules of 128 protein-DNA interfaces have been analyzed. Although these are less planar, like the protein-protein interfaces, the protein-DNA interfaces can also be dissected into core regions in ... -
Disulfide bonds, their stereospecific environment and conservation in protein structures
(OXFORD UNIV PRESS, 2004-11)We studied the specificity of the non-bonded interaction in the environment of 572 disulfide bonds in 247 polypeptide chains selected from the Protein Data Bank. The preferred geometry of interaction of peptide oxygen atoms ... -
The effect of zinc oxide nanoparticles on the structure of the periplasmic domain of the Vibrio cholerae ToxR protein
(WILEY-BLACKWELL, 2010-10)Proteins adsorbed on nanoparticles (NPs) are being used as biosensors and in drug delivery. However, our understanding of the effect of NPs on the structure of proteins is still in a nascent state. In this work we report ... -
Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes
(SPRINGER, 2009-09)We report a simple algorithm to scan interfaces in protein-protein complexes for identifying binding 'hot spots'. The change in side-chain solvent accessible area (ΔASA) of interface residues has been related to change in ... -
Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif
(ELSEVIER, 2007-09-18)dentification of sequence motifs that favor cis peptide bonds in proteins is important for understanding and designing proteins containing turns mediated by cis peptide conformations. From H-1 NMR solution studies on short ... -
Geometry of nonbonded interactions involving planar groups in proteins
(PERGAMON-ELSEVIER SCIENCE LTD, 2007-09)Although hydrophobic interaction is the main contributing factor to the stability of the protein fold, the specificity of the folding process depends on many directional interactions. An analysis has been carried out on ... -
Hydration of protein-protein interfaces
(WILEY-BLACKWELL, 2005-07-01)We present an analysis of the water molecules immobilized at the protein-protein interfaces of 115 homodimeric proteins and 46 protein-protein complexes, and compare them with 173 large crystal packing interfaces representing ... -
Interaction geometry involving planar groups in protein-protein interfaces
(WILEY-BLACKWELL, 2007-04)The geometry of interactions of planar residues is nonrandom in protein tertiary structures and gives rise to conventional, as well as nonconventional. (X-H center dot center dot center dot pi, X-H center dot center dot ... -
Interresidue contacts in proteins and protein-protein interfaces and their use in characterizing the homodimeric interface
(AMER CHEMICAL SOC, 2005-09)The environment of amino acid residues in protein tertiary structures and three types of interfaces formed by protein-protein association-in complexes, homodimers, and crystal lattices of monomeric proteins-has been analyzed ... -
Intgeom: A server for the calculation of the interaction geometry between planar groups in proteins
(OMICS Pub., 2009-01)IntGeom is a server for the calculation of the relative orientation between any two planar groups in protein side chains. IntGeom1 considers ten planar groups, while IntGeom2 is meant for studying the contact between a ... -
A lethal cardiotoxic-cytotoxic protein from the Indian monocellate cobra (Naja kaouthia) venom
(PERGAMON-ELSEVIER SCIENCE LTD, 2010-09-15)A lethal cardiotoxic-cytotoxic protein (mol wt. 6.76 kDa) has been purified from the Indian monocellate cobra (Naja kaouthia) venom by ion-exchange chromatography and HPLC. CD spectra indicated the presence of 23% alpha ... -
Macromolecular recognition in the Protein Data Bank
(WILEY-BLACKWELL, 2007-01)Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein-protein and protein DNA complexes and permanent assemblies in ... -
Parity in the number of atoms in residue composition in proteins and contact preferences
(CURRENT SCIENCE ASSN, 2006-02-25)Two ways of looking into the amino acid composition in a database - one based on counting residues and another on the number of atoms each residue contributes to the total - give quite different results. In the former, the ...