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

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

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.
Venue
Nucleic Acids Research
Published
2006-07-01
Volume
34
Issue
Web Server
Pages
W116-W118
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
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
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
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › 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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