ArticleProtein science : a publication of the Protein Society2005
Identification of the ligand binding sites on the molecular surface of proteins.
Article in Protein science : a publication of the Protein Society, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Drug Discovery Strategies for Kallikrein-Related Peptidases.International journal of molecular sciences · 2025Review
- Evolutionary and Functional Insights of Leucine-Rich Alpha-2-Glycoprotein 1 in Cetacean Wound Healing: The First Identification of LRG1 in the Bottlenose Dolphin (Tursiops truncatus).Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Article
- Article
- In silico analysis and molecular identification of an anaphase-promoting complex homologue from human pathogen Entamoeba histolytica.Journal, genetic engineering & biotechnology · 2021Article
- Computational elucidation of the binding mechanisms of curcumin analogues as bacterial RecA inhibitors.RSC advances · 2019Article
- Sertraline, chlorprothixene, and chlorpromazine characteristically interact with the REST-binding site of the corepressor mSin3, showing medulloblastoma cell growth inhibitory activities.Scientific reports · 2018Article
- Discovery of Nicotinamide Adenine Dinucleotide Binding Proteins in the Escherichia coli Proteome Using a Combined Energetic- and Structural-Bioinformatics-Based Approach.Journal of proteome research · 2017Article
- Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs.Scientific reports · 2016Article
- Theoretical analyses on a flipping mechanism of UV-induced DNA damage.Biophysics and physicobiology · 2016Article
- Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.Bioinformatics (Oxford, England) · 2015Article
- PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions.International journal of molecular sciences · 2014Article
- VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials.PLoS computational biology · 2014Article
- Exhaustive comparison and classification of ligand-binding surfaces in proteins.Protein science : a publication of the Protein Society · 2013Article
- Local functional descriptors for surface comparison based binding prediction.BMC bioinformatics · 2012Article
- Modeling regionalized volumetric differences in protein-ligand binding cavities.Proteome science · 2012Article
- Structure- and sequence-based function prediction for non-homologous proteins.Journal of structural and functional genomics · 2012Article
- Accuracy of functional surfaces on comparatively modeled protein structures.Journal of structural and functional genomics · 2011Article
- Ligand-binding site prediction of proteins based on known fragment-fragment interactions.Bioinformatics (Oxford, England) · 2010Article
- eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.Nucleic acids research · 2007Article
- LigProf: a simple tool for in silico prediction of ligand-binding sites.Journal of molecular modeling · 2007Article
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2 authors.
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Abstract
Identification of protein biochemical functions based on their three-dimensional structures is now required in the post-genome-sequencing era. Ligand binding is one of the major biochemical functions of proteins, and thus the identification of ligands and their binding sites is the starting point for the function identification. Previously we reported our first trial on structure-based function prediction, based on the similarity searches of molecular surfaces against the functional site database. Here we describe the extension of our first trial by expanding the search database to whole heteroatom binding sites appearing within the Protein Data Bank (PDB) with the new analysis protocol. In addition, we have determined the similarity threshold line, by using 10 structure pairs with solved free and complex structures. Finally, we extensively applied our method to newly determined hypothetical proteins, including some without annotations, and evaluated the performance of our methods.
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