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Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
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Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to

M Karthikeyan1, S Krishnan, Anil Kumar Pandey

  • 1Digital Information Resource Center, Information Division, National Chemical Laboratory, Pune 411008, India. m.karthikeyan@ncl.res.in

Journal of Chemical Information and Modeling
|April 12, 2008
PubMed
Summary
This summary is machine-generated.

ChemStar offers an open-source, distributed chemical computing environment using Java Remote Method Invocation (RMI). This flexible architecture enables large-scale property calculations and comparisons, aiding drug discovery research.

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Area of Science:

  • Computational Chemistry
  • Cheminformatics
  • Software Architecture

Background:

  • Distributed computing offers a powerful paradigm for tackling large-scale computational chemistry problems.
  • Existing frameworks may lack flexibility or open-source accessibility for diverse computational tasks.
  • The ChemXtreme project demonstrated the utility of Java RMI for distributed data harvesting.

Purpose of the Study:

  • To present ChemStar, a novel open-source distributed chemical computing environment.
  • To demonstrate the adaptability of a Java RMI-based architecture for parallelizable computational tasks.
  • To compare chemical property calculations (log P, TPSA) between different software packages on a large dataset.

Main Methods:

  • Development of a Java RMI-based server/client framework for distributed computing.
  • Implementation of a large-scale application for calculating chemical properties of PubChem compounds.
  • Utilized Marvin toolkit and JOELib package for property predictions.
  • Comparison of calculated log P and TPSA values between the two packages.

Main Results:

  • ChemStar successfully enabled distributed computation of chemical properties for approximately 18 million compounds.
  • Comparison revealed agreement in log P and TPSA values between Marvin and JOELib, with outliers often being non-druglike compounds.
  • Differences in calculated properties were generally attributable to variations in underlying algorithms.

Conclusions:

  • ChemStar is the first open-source distributed chemical computing environment utilizing Java RMI.
  • Its plug-in architecture ensures adaptability to various computational demands.
  • The platform facilitates large-scale chemical property analysis and cross-package validation, supporting drug discovery efforts.