Cited by 2,389Protein Structure and DynamicsEnzyme Structure and FunctionComputational Drug Discovery Methods

CASTp 3.0: computed atlas of surface topography of proteins

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Tian, Wei, Chen, Chang, Lei, Xue, Zhao, Jieling, Liang, Jie·2018·Nucleic Acids Research

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 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.”

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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
Published
2018-06-01
Volume
46
Issue
W1
Pages
W363-W367
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
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
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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