Phosphate binding sites identification in protein structures.
Nearly half of known protein structures interact with phosphate-containing ligands, such as nucleotides and other cofactors. Many methods have been developed for the identification of metal ions-binding sites and some for bigger ligands such as carbohydrates, but none is yet available for the prediction of phosphate-binding sites. Here we describe Pfinder, a method that predicts binding sites for phosphate groups, both in the form of ions or as parts of other non-peptide ligands, in proteins of known structure. Pfinder uses the Query3D local structural comparison algorithm to scan a protein structure for the presence of a number of structural motifs identified for their ability to bind the phosphate chemical group. Pfinder has been tested on a data set of 52 proteins for which both the apo and holo forms were available. We obtained at least one correct prediction in 63% of the holo structures and in 62% of the apo. The ability of Pfinder to recognize a phosphate-binding site in unbound protein structures makes it an ideal tool for functional annotation and for complementing docking and drug design methods. The Pfinder program is available at http://pdbfun.uniroma2.it/pfinder.
Parca
Luca
L
Department of Biology, Centre for Molecular Bioinformatics, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy.
Gherardini
Pier Federico
PF
Helmer-Citterich
Manuela
M
Ausiello
Gabriele
G
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D008024:Ligands; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D010710:Phosphates / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012984:Software
D000596:Amino Acids; D008024:Ligands; D010710:Phosphates; D011506:Proteins