ArticleNucleic acids research2018
CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers.
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Who cites it
157 citing papers in PubMed.
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- Conformational signatures of native ligand and pharmacochaperone binding in rhodopsin.Structure (London, England : 1993) · 2026Article
- De novo generation and computational screening of dual-targeting short peptide inhibitors against PBP2b and PBP2x in drug-resistant Streptococcus Pneumoniae.Molecular diversity · 2026Article
- Structure-coevolution dual-guided engineering of C-glycosyltransferase enables high-level biosynthesis of vitexin inSynthetic and systems biotechnology · 2026Article
- Substrate-Guided Engineering of Imine Reductases: A Strategy for Synthesizing Tertiary Amine N-Heterocycles.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- Ginkgolide B drives TCA cycle to accelerate Streptococcus suis biofilm dissociation.Archives of microbiology · 2026Article
- Lippia umbellata Cav.: Chemical Composition, Insecticidal, and Antimicrobial Activities.Chemistry & biodiversity · 2026Article
- Can Cavity Prediction Algorithms Help in Docking Experiments?Journal of computational chemistry · 2026Article
- Antibacterial and anti-biofilm mechanisms of 1,8-cineole against colistin-resistant Acinetobacter baumannii: an integrated in vitro, gene expression, and in silico study.Scientific reports · 2026Article
- Structure-Based Strategy Reveals a Novel Ligand Binding Site inACS omega · 2026Article
- Breaking glycolysis: allosteric hotspots for multi-target drug repurposing.Journal of computer-aided molecular design · 2026Article
- A systematic evaluation of protein allosteric site prediction tools with independent datasets.Journal of computer-aided molecular design · 2026Article
- Selective Anti-Giardial Action of Indirubin: Biochemical and Functional Evidence for Inhibition of Triosephosphate Isomerase and Aldose Reductase inInternational journal of molecular sciences · 2026Article
- Single versus mixed perfluorinated compound exposures and cardiovascular disease risk: mechanistic insights from cross-sectional data and molecular interactions.Archives of toxicology · 2026Article
- Integrated transcriptomic and molecular docking analysis identifies Rhotekin 2 as a promising therapeutic target for overcoming gemcitabine resistance in cholangiocarcinoma.Biomedical reports · 2026Article
- Inosine promotes erythrocyte metabolic reprogramming and restores oxygen release for rejuvenation via 2,3-BPG-PNP axis.Cell discovery · 2026Article
- Unveiling a catalytically promiscuous feruloyl esterase from Clostridium acetobutylicum.Applied microbiology and biotechnology · 2026Article
- Decoding Allosteric Inhibition in MALT1: The Hidden Role of Conformational Plasticity in Metastable States via Biased MD and Deep Learning.The journal of physical chemistry. B · 2026Article
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
97 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
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Abstract
CavityPlus is a web server that offers protein cavity detection and various functional analyses. Using protein three-dimensional structural information as the input, CavityPlus applies CAVITY to detect potential binding sites on the surface of a given protein structure and rank them based on ligandability and druggability scores. These potential binding sites can be further analysed using three submodules, CavPharmer, CorrSite, and CovCys. CavPharmer uses a receptor-based pharmacophore modelling program, Pocket, to automatically extract pharmacophore features within cavities. CorrSite identifies potential allosteric ligand-binding sites based on motion correlation analyses between cavities. CovCys automatically detects druggable cysteine residues, which is especially useful to identify novel binding sites for designing covalent allosteric ligands. Overall, CavityPlus provides an integrated platform for analysing comprehensive properties of protein binding cavities. Such analyses are useful for many aspects of drug design and discovery, including target selection and identification, virtual screening, de novo drug design, and allosteric and covalent-binding drug design. The CavityPlus web server is freely available at http://repharma.pku.edu.cn/cavityplus or http://www.pkumdl.cn/cavityplus.
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