New HierS scaffold analyis library released with source code

Dear Colleagues,

This new scaffold analysis library, implementing the HierS algorithm published by Wilkens et al., and built with JChem, is relased as an open-source project via Google Code, with the project home page at http://code.google.com/p/unm-biocomp-hscaf/.  It is hoped that this code will be useful to others in the ChemAxon user community.  We are mindful that a HierS package was contributed previously (forum topic 710) but not open-source.

As always we are very grateful to ChemAxon for their excellent software, support, academic licensing and fostering a vibrant worldwide user community.

Jeremy Yang
University of New Mexico Division of Biocomputing

 

 

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The following is excerpted from the project home page:

Introduction

Java package edu.unm.health.biocomp.hscaf, from the University of New Mexico Division of Biocomputing, is an open-source library built upon the JChem toolkit from ChemAxon,
for chemical scaffold analysis, for single molecules, datasets, or
common-scaffold comparisons between pairs or groups of molecules.

Features

• The HierS hierarchical scaffolds algorithm published by Wilkens et al. (2005) is implemented.


• This library is dependent on cheminformatics toolkit JChem from ChemAxon Ltd.


• Individual molecules or large datasets can be analyzed.


• Scaffold
  trees define a comprehensive set of scaffolds for a molecule, the
  largest of which corresponds to the Bemis-Murcko framework.


• Common scaffolds between two molecules can be identified.


• Analyze a molecule and identify all scaffolds, linkers and side-chains.


• Scaffold attachment points can be identified.


• Unique sets of scaffolds for a molecule or for a dataset of many molecules can be found.


• The hierarchical scaffold tree for a molecule can be generated.


• An
  N-attached variant of the HierS scaffold definition may be used, where
  atoms single-bonded to ring nitrogens are considered part of the
  scaffold.


• Optionally scaffolds may be stereo or (by default) non-stereo.


• Maximum common scaffold of two molecules, maximum common subtrees of two scaffold trees.

Author

• Jeremy Yang

Prerequisites

• Java 1.6 (SE6)


• ChemAxon JChem 5.5.0+

Documentation

• API (Javadoc)


• Getting Started

Support

This software is provided as-is, with no warranty and no support commitment.

License

This code released under terms of the New BSD EULA.

Acknowledgements

• This
  software project was partially funded via NIH award 1R21GM095952-01,
  "Chemical Pattern Detection and Visualization in Biological Networks",
  PI Tudor Oprea.


• Includes source code for class ShortestPath, written by Miklos Vargyas, ChemAxon, and obtained from the ChemAxon forum.


• Thanks
  to the fine work and 2005 publication of the HierS algorithm by Steven
  J. Wilkens, Jeff Janes and Andrew I. Su, of the Genomics Institute of
  the Novartis Research Foundation.

References

1. HierS: Hierarchical Scaffold Clustering, Steven J. Wilkens, Jeff Janes, Andrew I. Su, J. Med. Chem. 2005, 48, 3182-3193.


2. ChemAxon Ltd., Budapest, Hungary.