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CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds
Open accessPreprint — published as 10.1093/nar/gkae415 · Paper page
Abstract
Geometric and topological properties of protein structures, including surface pockets, interior cavities, and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a widely used web server for locating, delineating, and measuring these geometric and topological properties of protein structures. Recent developments in AI-based protein structure prediction such as AlphaFold2 (AF2) have significantly expanded our knowledge on protein structures. Here we present CASTpFold, a continuation of CASTp that provides accurate and comprehensive identifications and quantifications of protein topography. It now provides (i) results on an expanded database of proteins, including the Protein Data Bank (PDB) and non-singleton representative structures of AlphaFold2 structures, covering 183 million AF2 structures; (ii) functional pockets prediction with corresponding Gene Ontology (GO) terms or Enzyme Commission (EC) numbers for AF2-predicted structures; and (iii) pocket similarity search function for surface and protein-protein interface pockets. The CASTpFold web server is freely accessible at https://cfold.bme.uic.edu/castpfold/ .
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Metadata
- Authors
- Ye, B., Tian, W., Wang, B., & Liang, J.
- Affiliations
- University of Illinois Chicago (US)
- Salk Institute for Biological Studies (US)
- The University of Texas Southwestern Medical Center (US)
- Corresponding author
- Liang, Jie
- Venue
- Nucleic Acids Research
- Publisher
- openRxiv
- Published
- 2024-05-06
- Volume
- 52
- Issue
- W1
- Pages
- W194-W199
- ISSN
- 0305-1048 (ISSN-L)
- PMC
- PMC11223844
- OpenAlex
- W4398761928
- Cited by
- 181
- References
- 1
- Citations by year
- 2026: 113 · 2025: 59 · 2024: 9
- FWCI
- 24.57
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R35GM127084)
- Topics
- 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
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- protein cavities, protein-protein interfaces, AlphaFold2, Gene Ontology, enzyme commission numbers
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