ReviewBioorganic & medicinal chemistry letters2015
Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function.
Review in Bioorganic & medicinal chemistry letters, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed.
- Article
- Entabolons: How Metabolites Modify the Biochemical Function of Proteins and Cause the Correlated Behavior of Proteins in Pathways.Journal of chemical information and modeling · 2025Review
- GraphSite: Ligand Binding Site Classification with Deep Graph Learning.Biomolecules · 2022Article
- Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace.Briefings in bioinformatics · 2021Review
- Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 fromPeerJ · 2021Article
- BionoiNet: ligand-binding site classification with off-the-shelf deep neural network.Bioinformatics (Oxford, England) · 2020Article
- Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.Journal of computer-aided molecular design · 2019Article
- High Impact: The Role of Promiscuous Binding Sites in Polypharmacology.Molecules (Basel, Switzerland) · 2019Article
- 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns.International journal of molecular sciences · 2019Article
- Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs.Medicinal research reviews · 2019Review
- In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery.Journal of computer-aided molecular design · 2018Article
- Exploring a new ligand binding site of G protein-coupled receptors.Chemical science · 2018Article
- Article
- Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins.Scientific reports · 2017Article
- Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants.ACS chemical biology · 2017Article
- Catalytic and substrate promiscuity: distinct multiple chemistries catalysed by the phosphatase domain of receptor protein tyrosine phosphatase.The Biochemical journal · 2016Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Coincidence of the properties of ligand binding pockets in native proteins with those in proteins generated by computer simulations without selection for function shows that pockets are a generic protein feature and the number of distinct pockets is small. Similar pockets occur in unrelated protein structures, an observation successfully employed in pocket-based virtual ligand screening. The small number of pockets suggests that off-target interactions among diverse proteins are inherent; kinases, proteases and phosphatases show this prototypical behavior. The ability to repurpose FDA approved drugs is general, and minor side effects cannot be avoided. Finally, the implications to drug discovery are explored.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.