ArticleProtein science : a publication of the Protein Society2011
Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library.
Article in Protein science : a publication of the Protein Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Cytotoxic Activity of Halymenia durvillaei against Cervical Cancer Cells: In Vitro and Computational Evidence.Cell biochemistry and biophysics · 2026Article
- Cobdock: an accurate and practical machine learning-based consensus blind docking method.Journal of cheminformatics · 2024Article
- Article
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- Isolation of phytochemical constituents fromHeliyon · 2021Article
- Quercetin and/or Ascorbic Acid Modulatory Effect on Phenobarbital-Induced Sleeping Mice Possibly through GABAPharmaceuticals (Basel, Switzerland) · 2021Article
- Molecular optimization, docking, and dynamic simulation profiling of selective aromatic phytochemical ligands in blocking the SARS-CoV-2 S protein attachment to ACE2 receptor: anJournal of advanced veterinary and animal research · 2021Article
- Withanone fromDrug design, development and therapy · 2021Article
- NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence.Protein science : a publication of the Protein Society · 2020Article
- Investigating the Binding Mode of Reversible LSD1 Inhibitors Derived from Stilbene Derivatives by 3D-QSAR, Molecular Docking, and Molecular Dynamics Simulation.Molecules (Basel, Switzerland) · 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
- Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database.BMC bioinformatics · 2018Article
- Computational methods in drug discovery.Beilstein journal of organic chemistry · 2016Review
- myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.Biophysics and physicobiology · 2016Article
- Isolation, characterization and antifungal docking studies of wortmannin isolated from Penicillium radicum.Scientific reports · 2015Article
- Pocket-based drug design: exploring pocket space.The AAPS journal · 2013Review
- Bioinformatics and variability in drug response: a protein structural perspective.Journal of the Royal Society, Interface · 2012Review
- Identification of alternative binding sites for inhibitors of HIV-1 ribonuclease H through comparative analysis of virtual enrichment studies.Journal of chemical information and modeling · 2011Article
- Novel allosteric sites on Ras for lead generation.PloS one · 2011Article
- A GU-Net-Based Architecture Predicting Ligand-Protein-Binding Atoms.Journal of medical signals and sensorsArticle
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A new approach to predicting the ligand-binding sites of proteins was developed, using protein-ligand docking computation. In this method, many compounds in a random library are docked onto the whole protein surface. We assumed that the true ligand-binding site would exhibit stronger affinity to the compounds in the random library than the other sites, even if the random library did not include the ligand corresponding to the true binding site. We also assumed that the affinity of the true ligand-binding site would be correlated to the docking scores of the compounds in the random library, if the ligand-binding site was correctly predicted. We call this method the molecular-docking binding-site finding (MolSite) method. The MolSite method was applied to 89 known protein-ligand complex structures extracted from the Protein Data Bank, and it predicted the correct binding sites with about 80-99% accuracy, when only the single top-ranked site was adopted. In addition, the average docking score was weakly correlated to the experimental protein-ligand binding free energy, with a correlation coefficient of 0.44.
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