CASTp 3.0: computed atlas of surface topography of proteins
Open accessAbstract
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 web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.
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Pocket residues directly outlining the cavity (calculated by CASTp) are highly conserved between pAHR and hAHR, with 24 out of 26 residues fully identical.
“According to the ligand-bound complex structures and the sequence alignment of pAHR and hAHR (Fig. 3b and Supplementary Fig. 1b), pocket residues directly outlining the cavity (calculated by CASTp algorithm41) are highly conserved among these two species, with 24 out of 26 residues fully identical.”
From Structural basis for the ligand-dependent activation of heterodimeric AHR-ARNT complex (2025) · cites this paper as [41]
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“1b), pocket residues directly outlining the cavity (calculated by CASTp algorithm 41 ) are highly conserved among these two species, with24 out of 26 residues fully identical.”
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- Authors
- Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J.
- Affiliations
- University of Illinois Chicago (US)
- Institut national de recherche en sciences et technologies du numérique (FR)
- Corresponding author
- Liang, Jie
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-06-01
- Volume
- 46
- Issue
- W1
- Pages
- W363-W367
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6031066
- OpenAlex
- W4255677297
- Cited by
- 2,389
- References
- 32
- Citations by year
- 2026: 239 · 2025: 374 · 2024: 420 · 2023: 390 · 2022: 367 · 2021: 290 · 2020: 202 · 2019: 94 · 2018: 10 · 2014: 1
- FWCI
- 52.72
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- Figshare (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health (R01CA204962)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein channels, web server, protein structure analysis, biological assemblies, secondary structure, functional sites
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