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A grid service‐based workflow for in‐silico screening of chemical inhibitors of phosphatases
Author(s) -
Levesque Marshall,
Chien Shu,
Haga Jason
Publication year - 2008
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.22.1_supplement.756.15
Subject(s) - computer science , workflow , grid computing , grid , virtual screening , scalability , testbed , dock , distributed computing , workflow management system , supercomputer , database , operating system , world wide web , chemistry , drug discovery , biochemistry , geometry , mathematics
In many cases, grid computing offers the powerful alternative of sharing resources on a worldwide scale, across a number of different institutions to run computationally intensive applications without the need for a large, centralized supercomputer. This paper presents a scalable, reusable workflow assembled to choreograph large virtual screening experiments over a computational Grid using the molecular docking application DOCK. Software components were applied on multiple levels to create automated workflows that perform data delivery, job scheduling, job status query, and the collection of results to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP to wrap the application as a Grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of Grid infrastructure and security. With the workflow in place, a screening was performed with the ZINC 2,066,906 ligand “druglike” subset database against the catalytic site of the phosphatase SHP‐1 using the MPI version of DOCK 5.4 on the PRAGMA Grid testbed, utilizing 200 processors over 7 clusters. This is the first successful use of Grid computing to identify chemical inihibitors of enzymatic activity through virtual screening. This project was supported by PRIME (NSF 0407508), PRIUS, PRAGMA, and Calit2.