PDBparam: Online Resource for Computing Structural Parameters of Proteins.

PDBparam: Online Resource for Computing Structural Parameters of Proteins. Bioinform Biol Insights. 2016;10:73-80 Authors: Nagarajan R, Archana A, Thangakani AM, Jemimah S, Velmurugan D, Gromiha MM 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 ...
Source: Bioinformatics and Biology Insights - Category: Bioinformatics Authors: Tags: Bioinform Biol Insights Source Type: research

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