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

Project Activity

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Categories

Bio-Informatics

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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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