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CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome
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Abstract
Location and properties of ligand binding sites provide important information to uncover protein functions and to direct structure-based drug design approaches. However, as binding site detection depends on the three-dimensional (3D) structural data of proteins, functional analysis based on protein ligand binding sites is formidable for proteins without structural information. Recent developments in protein structure prediction and the 3D structures built by AlphaFold provide an unprecedented opportunity for analyzing ligand binding sites in human proteins. Here, we constructed the CavitySpace database, the first pocket library for all the proteins in the human proteome, using a widely-applied ligand binding site detection program CAVITY. Our analysis showed that known ligand binding sites could be well recovered. We grouped the predicted binding sites according to their similarity which can be used in protein function prediction and drug repurposing studies. Novel binding sites in highly reliable predicted structure regions provide new opportunities for drug discovery. Our CavitySpace is freely available and provides a valuable tool for drug discovery and protein function studies.
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Metadata
- Authors
- Wang, S., Lin, H., Huang, Z., He, Y., Deng, X., Xu, Y., Pei, J., & Lai, L.
- Affiliations
- Peking University (CN)
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Corresponding author
- Pei, Jianfeng
- Lai, Luhua
- Venue
- Biomolecules
- Publisher
- MDPI AG
- Published
- 2022-07-11
- Volume
- 12
- Issue
- 7
- Pages
- 967
- ISSN
- 2218-273X (ISSN-L)
- PMC
- PMC9312471
- OpenAlex
- W4285020367
- Cited by
- 39
- References
- 41
- Citations by year
- 2026: 3 · 2025: 10 · 2024: 13 · 2023: 8 · 2022: 5
- FWCI
- 5.00
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Biomolecules (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- the National Natural Science Foundation of China (22033001, 2021-I2M-5-014)
- the Chinese Academy of Medical Sciences (22033001, 2021-I2M-5-014)
- Topics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- ligand binding sites, human proteome, protein binding site prediction, cavities, AlphaFold, protein structure prediction, protein function prediction, drug repurposing, structure-based drug design
- MeSH terms
- Binding Sites, Humans, Ligands, Protein Binding, Proteome, Biophysical Phenomena
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