title: PDBparam: Online Resource for Computing Structural Parameters of Proteins.
abstract: Understanding the structure-function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in the literature, no single server can calculate a wide-ranging set of structure-based features from protein three-dimensional structures. In this work, we have developed a web-based tool, PDBparam, for computing more than 50 structure-based features for any given protein structure. These features are classified into four major categories: (i) interresidue interactions, which include short-, medium-, and long-range interactions, contact order, long-range order, total contact distance, contact number, and multiple contact index, (ii) secondary structure propensities such as α-helical propensity, β-sheet propensity, and propensity of amino acids to exist at various positions of α-helix and amino acid compositions in high B-value regions, (iii) physicochemical properties containing ionic interactions, hydrogen bond interactions, hydrophobic interactions, disulfide interactions, aromatic interactions, surrounding hydrophobicity, and buriedness, and (iv) identification of binding site residues in protein-protein, protein-nucleic acid, and protein-ligand complexes. The server can be freely accessed at http://www.iitm.ac.in/bioinfo/pdbparam/. We suggest the use of PDBparam as an effective tool for analyzing protein structures.
authors.affiliation: Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
authors.forename: R
authors.initials: R
authors.lastname: Nagarajan
authors.affiliation: Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
authors.forename: A
authors.initials: A
authors.lastname: Archana
authors.affiliation: CAS in Crystallography and Biophysics, University of Madras, Chennai, India.; Bioinformatics Infrastructure Facility, University of Madras, Chennai, India.
authors.forename: A Mary
authors.initials: AM
authors.lastname: Thangakani
authors.affiliation: Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
authors.forename: S
authors.initials: S
authors.lastname: Jemimah
authors.affiliation: CAS in Crystallography and Biophysics, University of Madras, Chennai, India.; Bioinformatics Infrastructure Facility, University of Madras, Chennai, India.
authors.forename: D
authors.initials: D
authors.lastname: Velmurugan
authors.affiliation: Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
authors.forename: M Michael
authors.initials: MM
authors.lastname: Gromiha
keywords: binding sites; physicochemical properties; protein three-dimensional structure; secondary structure propensity