The Computed Atlas of Surface Topography of proteins (CASTp) server uses the alpha shape method (4 ) developed in computational geometry to identify topographic features, to measure area and volume and to compute imprint (5–8 (link)). The alpha shape method has also been applied in other studies of cavities and channels in protein structures (9 (link),10 (link)). The secondary structures are calculated using DSSP (11 (link)). Residue annotations of proteins are obtained from UniProt database (12 (link)) and mapped to PDB structures with residue-level information from the SIFTS database (13 (link)). The biological assemblies are extracted from the .mmicf files of the PDB database. Only the assemblies with biological significance and designated by the authors of the PDB structures (http://mmcif.wwpdb.org ) are processed and listed on the CASTp server.
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Protein Surface Topography Analysis
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Biological
Cavities
Imprint
Protein
Proteins annotations
Surface proteins
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Protocol cited in 327 other protocols
Variable analysis
independent variables
- Alpha shape method
- UniProt database
- SIFTS database
- Biological assemblies extracted from .mmicf files of the PDB database
- Identification of topographic features
- Measurement of area and volume
- Computation of imprint
- Calculation of secondary structures
- Only biological assemblies with significance and designated by the authors of the PDB structures are processed and listed on the CASTp server
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