JSiteDescriptor

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

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Additional Project Details

Intended Audience

Science/Research

User Interface

Java Swing

Programming Language

Java

Related Categories

Java Bio-Informatics Software

Registered

2012-02-05

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