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A set of java programs that extract coordinate and chemical information from PDB files.
The binding site regions are extracted using grid based scheme.
For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too).
Features
- Generation of PocketMatch based vector descriptor for a binding site
- Running in single PDB file mode or Batch mode
- Specification of site as ligand neighbourhood - (Ligand code, name and chain ID)
- Specification of site as PDB subset neighbourhood using REGULAR EXPRESSIONS
- Specification of multiple ranges of atoms lining a binding site
- Batch mode processing file captures input parameters through XML file + conforming to XSD specification
- Greater configurability - residue group selection, radius and categories for sites
- Java Swing technology for GUI
- Simple and extensible software architecture for future development
Categories
Bio-InformaticsFollow JSiteDescriptor
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