ArticleProtein science : a publication of the Protein Society2011
Toward prediction of functional protein pockets using blind docking and pocket search algorithms.
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 29 papers.
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29 citing papers in PubMed.
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- Docking in the Dark: Insights into Protein-Protein and Protein-Ligand Blind Docking.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Molecular chameleons adaptability in target binding.Structural dynamics (Melville, N.Y.) · 2025Article
- ProCV: A 3D similarity grouping method for enhanced protein pocket recognition and ligand interaction analysis.iScience · 2025Article
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- Testing Serum Albumins and Cyclodextrins as Potential Binders of the Mycotoxin Metabolites Alternariol-3-Sulfate, Alternariol-9-Monomethylether and Alternariol-9-Monomethylether-3-Sulfate.International journal of molecular sciences · 2022Article
- Exploration of Somatostatin Binding Mechanism to Somatostatin Receptor Subtype 4.International journal of molecular sciences · 2022Article
- Protein interactions with metallothionein-3 promote vectorial active transport in human proximal tubular cells.PloS one · 2022Article
- Integrated Computational Approaches and Tools forAllosteric Drug Discovery.International journal of molecular sciences · 2020Review
- Interaction of the mycotoxin metabolite dihydrocitrinone with serum albumin.Mycotoxin research · 2019Article
- Effects of point mutations in the binding pocket of the mouse major urinary protein MUP20 on ligand affinity and specificity.Scientific reports · 2019Article
- Towards Unraveling the Histone Code by Fragment Blind Docking.International journal of molecular sciences · 2019Article
- Interactions of zearalenone and its reduced metabolites α-zearalenol and β-zearalenol with serum albumins: species differences, binding sites, and thermodynamics.Mycotoxin research · 2018Article
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- Systematic exploration of multiple drug binding sites.Journal of cheminformatics · 2017Article
- Deciphering how Cpl-7 cell wall-binding repeats recognize the bacterial peptidoglycan.Scientific reports · 2017Article
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2 authors.
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Abstract
Location of functional binding pockets of bioactive ligands on protein molecules is essential in structural genomics and drug design projects. If the experimental determination of ligand-protein complex structures is complicated, blind docking (BD) and pocket search (PS) calculations can help in the prediction of atomic resolution binding mode and the location of the pocket of a ligand on the entire protein surface. Whereas the number of successful predictions by these methods is increasing even for the complicated cases of exosites or allosteric binding sites, their reliability has not been fully established. For a critical assessment of reliability, we use a set of ligand-protein complexes, which were found to be problematic in previous studies. The robustness of BD and PS methods is addressed in terms of success of the selection of truly functional pockets from among the many putative ones identified on the surfaces of ligand-bound and ligand-free (holo and apo) protein forms. Issues related to BD such as effect of hydration, existence of multiple pockets, and competition of subsidiary ligands are considered. Practical cases of PS are discussed, categorized and strategies are recommended for handling the different situations. PS can be used in conjunction with BD, as we find that a consensus approach combining the techniques improves predictive power.
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