title: PICI: A web server with a multi-parametric algorithm for identifying interaction sites within protein complexes.
abstract: Identifying interactions between proteins in a complex is essential to analyze their role in various cellular activities and structural stability. Therefore, effective algorithms and computer programs are required for the better understanding of various interactions exist at the protein-protein interface. The protein inter-chain interaction (PICI) server was developed to identify these interaction sites and various interactions that contribute to the specificity and strength of the protein complex by using Protein Interaction Identification Algorithm (PIIA). The multi-parametric approach of this algorithm involves the interface area between the subunits, the atomic coordinate distance, the linearity of bonds, the orientation of aromatic side-chains, and physicochemical properties of the residues. Particular advantages of PICI include its ability to identify various strong and weak interactions, including those which have not been considered before by any other server. Representation of interface data in text tables, 3D interaction visualizer, colored sequence viewer, and a dynamic colored graphical matrix display makes it distinct from similar web servers. Users can analyze interactions within multi-chain proteins by their PDBids or by uploading a structure atomic coordinate file and can download the result in plain text or XML format.
authors.affiliation: Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India.
authors.forename: Arindam Atanu
authors.initials: AA
authors.lastname: Das
authors.affiliation: Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India.
authors.forename: Ramadas
authors.initials: R
authors.lastname: Krishna