ArticleNucleic acids research2011
Phosphate binding sites identification in protein structures.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- On the emergence of metabolism: the evolution of proteins that powered life.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond.Briefings in bioinformatics · 2024Review
- Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Enhancing Top-Down Analysis Using Chromophore-Assisted Infrared Multiphoton Dissociation from (Phospho)peptides to Protein Assemblies.Analytical chemistry · 2020Article
- Simple yet functional phosphate-loop proteins.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.Nucleic acids research · 2013Article
- Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria.PLoS computational biology · 2013Article
- Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase.Journal of the American Chemical Society · 2012Article
- Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity.PloS one · 2012Article
- Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures.Journal of structural and functional genomics · 2011Review
- Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.Nucleic acids research · 2011Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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