Cited by 1,725Protein Structure and DynamicsEnzyme Structure and FunctionComputational Drug Discovery Methods

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CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

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Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., Liang, J.·2006·Nucleic Acids Research

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Abstract

Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp (http://cast.engr.uic.edu) is an online tool that locates and measures pockets and voids on 3D protein structures. This new version of CASTp includes annotated functional information of specific residues on the protein structure. The annotations are derived from the Protein Data Bank (PDB), Swiss-Prot, as well as Online Mendelian Inheritance in Man (OMIM), the latter contains information on the variant single nucleotide polymorphisms (SNPs) that are known to cause disease. These annotated residues are mapped to surface pockets, interior voids or other regions of the PDB structures. We use a semi-global pair-wise sequence alignment method to obtain sequence mapping between entries in Swiss-Prot, OMIM and entries in PDB. The updated CASTp web server can be used to study surface features, functional regions and specific roles of key residues of proteins.

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Authors: Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., & Liang, J.
Affiliations: University of Illinois Chicago (US)
Corresponding author: Dundas, J.
ORCID: Turpaz, Y.
Liang, J.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2006-07-01
Volume: 34
Issue: Web Server
Pages: W116-W118
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkl282
PMC: PMC1538779
OpenAlex: W2077776336
Cited by: 1,725
References: 8
Citations by year: 2026: 25 · 2025: 45 · 2024: 59 · 2023: 48 · 2022: 58 · 2021: 67 · 2020: 70 · 2019: 100 · 2018: 133 · 2017: 115 · 2016: 143 · 2015: 142 · 2014: 143 · 2013: 115 · 2012: 128
FWCI: 16.74
Type: journal article
Language: en
Open access: gold
doi.org
Licence: other-oa
Locations: Nucleic Acids Research (publishedVersion, other-oa)
PubMed (publishedVersion)
Funders: National Science Foundation (CAREER, 0133856)
Office of Naval Research (N00014-06-1-0100, N00014)
National Institute of General Medical Sciences (R01GM068958, GM 68958)
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: surface voids, protein cavities, OMIM, Swiss-Prot, sequence mapping, web server, protein structure
MeSH terms: Amino Acids, Computer Graphics, Protein Conformation, Proteins, Software, Sequence Alignment, Internet, Sequence Analysis, Protein, Polymorphism, Single Nucleotide, Databases, Protein

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CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

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