Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.

ABSTRACT: Phosfinder is a web server for the identification of phosphate binding sites in protein structures. Phosfinder uses a structural comparison algorithm to scan a query structure against a set of known 3D phosphate binding motifs. Whenever a structural similarity between the query protein and a phosphate binding motif is detected, the phosphate bound by the known motif is added to the protein structure thus representing a putative phosphate binding site. Predicted binding sites are then evaluated according to (i) their position with respect to the query protein solvent-excluded surface and (ii) the conservation of the binding residues in the protein family. The server accepts as input either the PDB code of the protein to be analyzed or a user-submitted structure in PDB format. All the search

SUBMITTER: Parca L 

PROVIDER: S-EPMC3125782 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature