Prof. Pinakpani Chakrabarti: Recent submissions
Now showing items 1-20 of 28
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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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
Structure of λ CII: Implications for recognition of direct-repeat DNA by an unusual tetrameric organization
(NATL ACAD SCIENCE, 2005-08-09)The temperate coliphage X, after infecting its host bacterium Escherichia coli, can develop either along the lytic or the lysogenic pathway. Crucial to the lysis/lysogeny decision is the homo tetrameric transcription-activator ... -
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 ... -
BioSuite: A comprehensive bioinformatics software package (A unique industry-academia collaboration)
(CURRENT SCIENCE ASSN, 2007-01-10) -
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 ... -
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 ... -
Peptide segments in protein-protein interfaces
(INDIAN ACADEMY SCIENCES, 2007-01)An important component of functional genomics involves the understanding of protein association. The interfaces resulting from protein-protein interactions - (i) specific, as represented by the homodimeric quaternary ... -
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 ... -
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 ... -
Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein-protein interactions
(OXFORD UNIV PRESS, 2007-08-01)Motivation: The increasing amount of data on protein-protein interaction needs to be rationalized for deriving guidelines for the alteration or design of an interface between two proteins. Results: We present a detailed ... -
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 ... -
Protein-protein interaction and quaternary structure
(CAMBRIDGE UNIV PRESS, 2008-05)Protein-protein recognition plays an essential role in structure and function. Specific non-covalent interactions stabilize the structure of macromolecular assemblies, exemplified in this review by oligomeric proteins and ... -
pi-Turns: types, systematics and the context of their occurrence in protein structures
(BIOMED CENTRAL LTD, 2008-09-22)Background: For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary ... -
Structural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes
(Biomedical Informatics, 2008-07-14)The interface of a protein molecule that is involved in binding another protein, DNA or RNA has been characterized in terms of the number of unique secondary structural segments (SSSs), made up of stretches of helix, strand ... -
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 ... -
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 ...