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Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W116-8.

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

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  • 1Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA.

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.

PMID:
16844972
PMCID:
PMC1538779
DOI:
10.1093/nar/gkl282
[PubMed - indexed for MEDLINE]
Free PMC Article
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