This is the Linux app named JSiteDescriptor to run in Linux online whose latest release can be downloaded as binaries.zip. It can be run online in the free hosting provider OnWorks for workstations.
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JSiteDescriptor to run in Linux online
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DESCRIPTION
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
Audience
Science/Research
User interface
Java Swing
Programming Language
Java
This is an application that can also be fetched from https://sourceforge.net/projects/jsitedescriptor/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
