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 [10.1093/nar/gkq987].

Phosphate binding sites identification in protein structures

HELMER CITTERICH, MANUELA;AUSIELLO, GABRIELE
2011-03

Abstract

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.
Pubblicato
Rilevanza internazionale
Articolo
Sì, ma tipo non specificato
Settore BIO/11
eng
Models, Molecular; Amino Acids; Protein Folding; Molecular Sequence Annotation; Protein Conformation; Software; Proteins; Phosphates; Ligands; Binding Sites; Algorithms
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 [10.1093/nar/gkq987].
Parca, L; Gherardini, P; HELMER CITTERICH, M; Ausiello, G
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2108/15046
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