ArticleJournal of molecular graphics & modelling2011
POVME: an algorithm for measuring binding-pocket volumes.
Article in Journal of molecular graphics & modelling, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
What it found
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Who cites it
113 citing papers in PubMed.
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- Identification of Protein Cryptic Sites via Conformational Dynamics Capturing and Water-Based Pocket Characterization in Molecular Dynamics Simulations.Journal of chemical theory and computation · 2025Article
- SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling.Proteins · 2025Article
- Allosteric modulation of NF1 GAP: Differential distributions of catalytically competent populations in loss-of-function and gain-of-function mutants.Protein science : a publication of the Protein Society · 2025Article
- Comparative evaluation of methods for the prediction of protein-ligand binding sites.Journal of cheminformatics · 2024Article
- Building shape-focused pharmacophore models for effective docking screening.Journal of cheminformatics · 2024Article
- CageCavityCalc (Journal of chemical information and modeling · 2024Article
- SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling.bioRxiv : the preprint server for biology · 2024Article
- On Inactivation of the Coronavirus Main Protease.Journal of chemical information and modeling · 2024Article
- QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.Chemical science · 2023Article
- Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations.Journal of chemical information and modeling · 2023Article
- In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein.ACS central science · 2023Article
- Decoding the secrets: how conformational and structural regulators inhibit the human 20S proteasome.Frontiers in chemistry · 2023Article
- Computational Identification of Potential Multitarget Inhibitors of Nipah Virus by Molecular Docking and Molecular Dynamics.Microorganisms · 2022Article
- Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics.PLoS computational biology · 2022Article
- Mechanistic insights into multiple-step transport of mitochondrial ADP/ATP carrier.Computational and structural biotechnology journal · 2022Article
- Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density.Molecules (Basel, Switzerland) · 2021Article
53 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Researchers engaged in computer-aided drug design often wish to measure the volume of a ligand-binding pocket in order to predict pharmacology. We have recently developed a simple algorithm, called POVME (POcket Volume MEasurer), for this purpose. POVME is Python implemented, fast, and freely available. To demonstrate its utility, we use the new algorithm to study three members of the matrix-metalloproteinase family of proteins. Despite the structural similarity of these proteins, differences in binding-pocket dynamics are easily identified.
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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.