Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem

Journal of Chemical Information and Modeling
M KarthikeyanAlexander Tropsha

Abstract

We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as w...Continue Reading

References

Jun 1, 1997·Current Opinion in Chemical Biology·J M Blaney, E J Martin
Apr 13, 2000·Journal of Chemical Information and Computer Sciences·F Csizmadia
Mar 30, 2001·Journal of Chemical Information and Computer Sciences·I V TetkoA E Villa
Feb 1, 2002·Nature Biotechnology·Meir GlickW Graham Richards
Jul 18, 2002·Nature Reviews. Drug Discovery·W Graham Richards
Oct 24, 2002·Journal of Computational Chemistry·E Keith DaviesW Graham Richards
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Christoph SteinbeckEgon Willighagen
Oct 19, 2005·Journal of Computer-aided Molecular Design·Igor V TetkoVolodymyr V Prokopenko
Nov 29, 2005·Journal of Chemical Information and Modeling·Paolo MazzatortaEmilio Benfenati
Mar 28, 2006·Journal of Chemical Information and Modeling·M KarthikeyanAndreas Bender
May 23, 2006·Journal of Chemical Information and Modeling·Sulev SildMati Karelson
May 23, 2006·Journal of Chemical Information and Modeling·Rajarshi GuhaEgon L Willighagen
May 23, 2006·Journal of Chemical Information and Modeling·Peter Lind, Markus Alm
Mar 27, 2007·Journal of Chemical Information and Modeling·Ewgenij ProschakUli Fechner

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