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

TitleDistributed chemical computing using chemstar: an open source java remote method invocation architecture applied to large scale molecular data from pubchem
Publication TypeJournal Article
Year of Publication2008
AuthorsKarthikeyan, M, Krishnan, S, Pandey, AKumar, Bender, A, Tropsha, A
JournalJournal of Chemical Information and Modeling
Volume48
Issue4
Pagination691-703
Date PublishedAPR
Type of ArticleArticle
ISSN1549-9596
Abstract

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 well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.nel.res.in/chemstar/.

DOI10.1021/ci700334f
Type of Journal (Indian or Foreign)Foreign
Impact Factor (IF)3.657
Divison category: 
Chemical Engineering & Process Development