The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Wolber, G., & Langer, T. (2005) · Journal of Chemical Information and Modeling · doi:10.1021/ci049885e · Cited by 1,954
The resurgence of covalent drugs
Singh, J., Petter, R. C., Baillie, T. A., & Whitty, A. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3410 · Cited by 1,873 · cited 1×
“About one third of the FDA approved drugs have been reported to act through covalent mechanisms (7,8).”
BackgroundQuantitative reactivity profiling predicts functional cysteines in proteomes
Weerapana, E., Wang, C., Simon, G. M., Richter, F., Khare, S., Dillon, M. B. D., Bachovchin, D. A., Mowen, K., Baker, D., & Cravatt, B. F. (2010) · Nature · doi:10.1038/nature09472 · Cited by 1,684
Wang, R., Fang, X., Lu, Y., & Wang, S. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm030580l · Cited by 1,133
Self-citationVery fast prediction and rationalization of p Ka values for protein–ligand complexes
Bas, D. C., Rogers, D. M., & Jensen, J. H. (2008) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22102 · Cited by 1,092
The PDBbind database: methodologies and updates
Wang, R., Fang, X., Lu, Y., Yang, C.-Y., & Wang, S. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm048957q · Cited by 933
Self-citationPharmacophore modeling and applications in drug discovery: challenges and recent advances
Yang, S.-Y. (2010) · Drug Discovery Today · doi:10.1016/j.drudis.2010.03.013 · Cited by 901
Gaussian Dynamics of Folded Proteins
Haliloglu, T., Bahar, I., & Erman, B. (1997) · Physical Review Letters · doi:10.1103/physrevlett.79.3090 · Cited by 772
Allostery in Disease and in Drug Discovery
Nussinov, R., & Tsai, C.-J. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 761
Developing Irreversible Inhibitors of the Protein Kinase Cysteinome
Liu, Q., Sabnis, Y., Zhao, Z., Zhang, T., Buhrlage, S. J., Jones, L. H., & Gray, N. S. (2013) · Chemistry & Biology · doi:10.1016/j.chembiol.2012.12.006 · Cited by 652
Cited by
AlphaFold, allosteric, and orthosteric drug discovery: Ways forward
Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2023) · Drug Discovery Today · doi:10.1016/j.drudis.2023.103551 · Cited by 96
Qin, X., Wang, R., Xu, H., Tu, L., Chen, H., Li, H., Liu, N., Wang, J., Li, S., Yin, F., et al. (2022) · Autophagy · doi:10.1080/15548627.2021.2022360 · Cited by 55
CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome
Wang, S., Lin, H., Huang, Z., He, Y., Deng, X., Xu, Y., Pei, J., & Lai, L. (2022) · Biomolecules · doi:10.3390/biom12070967 · Cited by 39
Self-citationCleavage of CAD by caspase-3 determines the cancer cell fate during chemotherapy
Ma, J., Zhao, J., Zhang, C., Tan, J., Cheng, A., Niu, Z., Lin, Z., Pan, G., Chen, C., Ding, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-60144-2 · Cited by 14
Metadata
- Authors
- Xu, Y., Wang, S., Hu, Q., Gao, S., Ma, X., Zhang, W., Shen, Y., Chen, F., Lai, L., & Pei, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-05-10
- Volume
- 46
- Issue
- W1
- Pages
- W374-W379
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2799327292
- Cited by
- 389
- References
- 28
- FWCI
- 17.58
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction. https://app.cochat.ai/papers/10.1093/nar/gky380
- The paper
- Xu, Y., Wang, S., Hu, Q., Gao, S., Ma, X., Zhang, W., Shen, Y., Chen, F., Lai, L., & Pei, J. (2018). CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction. Nucleic Acids Research. https://doi.org/10.1093/nar/gky380
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
