The webPDBinder (http://pdbinder.bio.uniroma2.it/PDBinder) is a web server for the identification of small ligand-binding sites in a protein structure. webPDBinder searches a protein structure against a library of known binding sites and a collection of control non-binding pockets. The number of similarities identified with the residues in the two sets is then used to derive a propensity value for each residue of the query protein associated to the likelihood that the residue is part of a ligand binding site. The predicted binding residues can be further refined using conservation scores derived from the multiple alignment of the PFAM protein family. webPDBinder correctly identifies residues belonging to the binding site in 77% of the cases and is able to identify binding pockets starting from holo or apo structures with comparable performances. This is important for all the real world cases where the query protein has been crystallized without a ligand and is also difficult to obtain clear similarities with bound pockets from holo pocket libraries. The input is either a PDB code or a user-submitted structure. The output is a list of predicted binding pocket residues with propensity and conservation values both in text and graphical format.

Bianchi, V., Mangone, I., Ferrè, F., HELMER CITTERICH, M., Ausiello, G. (2013). webPDBinder: a server for the identification of ligand binding sites on protein structures. NUCLEIC ACIDS RESEARCH, 41(Web Server issue), W308-W308-13 [10.1093/nar/gkt457].

webPDBinder: a server for the identification of ligand binding sites on protein structures

HELMER CITTERICH, MANUELA;AUSIELLO, GABRIELE
2013-06-03

Abstract

The webPDBinder (http://pdbinder.bio.uniroma2.it/PDBinder) is a web server for the identification of small ligand-binding sites in a protein structure. webPDBinder searches a protein structure against a library of known binding sites and a collection of control non-binding pockets. The number of similarities identified with the residues in the two sets is then used to derive a propensity value for each residue of the query protein associated to the likelihood that the residue is part of a ligand binding site. The predicted binding residues can be further refined using conservation scores derived from the multiple alignment of the PFAM protein family. webPDBinder correctly identifies residues belonging to the binding site in 77% of the cases and is able to identify binding pockets starting from holo or apo structures with comparable performances. This is important for all the real world cases where the query protein has been crystallized without a ligand and is also difficult to obtain clear similarities with bound pockets from holo pocket libraries. The input is either a PDB code or a user-submitted structure. The output is a list of predicted binding pocket residues with propensity and conservation values both in text and graphical format.
3-giu-2013
Pubblicato
Rilevanza internazionale
Articolo
Esperti anonimi
Settore BIO/11 - BIOLOGIA MOLECOLARE
English
Con Impact Factor ISI
Software; Models, Molecular; Proteins; Ligands; Internet; Protein Conformation; Binding Sites
Bianchi, V., Mangone, I., Ferrè, F., HELMER CITTERICH, M., Ausiello, G. (2013). webPDBinder: a server for the identification of ligand binding sites on protein structures. NUCLEIC ACIDS RESEARCH, 41(Web Server issue), W308-W308-13 [10.1093/nar/gkt457].
Bianchi, V; Mangone, I; Ferrè, F; HELMER CITTERICH, M; Ausiello, G
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/77520
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