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CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
Open accessAbstract
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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Metadata
- Authors
- Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., & Liang, J.
- Affiliations
- University of Illinois Chicago (US)
- Corresponding author
- Dundas, J.
- ORCID
- 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
- PMC
- PMC1538779
- OpenAlex
- W2077776336
- Cited by
- 1,725
- References
- 8
- Citations by year
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- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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