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, L., Gherardini, P.F., Helmer-Citterich, M., & Ausiello, G. (2011). Phosphate binding sites identification in protein structures. NUCLEIC ACIDS RESEARCH, 39(4), 1231-42.
|Tipologia:||Articolo su rivista|
|Citazione:||Parca, L., Gherardini, P.F., Helmer-Citterich, M., & Ausiello, G. (2011). Phosphate binding sites identification in protein structures. NUCLEIC ACIDS RESEARCH, 39(4), 1231-42.|
|Settore Scientifico Disciplinare:||Settore BIO/11|
|Revisione (peer review):||Sì, ma tipo non specificato|
|Digital Object Identifier (DOI):||http://dx.doi.org/10.1093/nar/gkq987|
|Stato di pubblicazione:||Pubblicato|
|Data di pubblicazione:||mar-2011|
|Titolo:||Phosphate binding sites identification in protein structures|
|Autori:||Parca, L; Gherardini, PF; Helmer-Citterich, M; Ausiello, G|
|Appare nelle tipologie:||01 - Articolo su rivista|