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Advanced Biological and Chemical Discovery (ABCD):  Centralizing Discovery Knowledge in an Inherently Decentralized World

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Information Technology, Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341, Information Technology, Johnson & Johnson Pharmaceutical Research & Development division of Janssen Pharmaceutica N.V., Turnhoutsweg 30, 2340 Beerse, Belgium, and Bioinformatics, Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 3210 Merryfield Row, San Diego, California 92121
Cite this: J. Chem. Inf. Model. 2007, 47, 6, 1999–2014
Publication Date (Web):November 1, 2007
Copyright © 2007 American Chemical Society

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    We present ABCD, an integrated drug discovery informatics platform developed at Johnson & Johnson Pharmaceutical Research & Development, L.L.C. ABCD is an attempt to bridge multiple continents, data systems, and cultures using modern information technology and to provide scientists with tools that allow them to analyze multifactorial SAR and make informed, data-driven decisions. The system consists of three major components:  (1) a data warehouse, which combines data from multiple chemical and pharmacological transactional databases, designed for supreme query performance; (2) a state-of-the-art application suite, which facilitates data upload, retrieval, mining, and reporting, and (3) a workspace, which facilitates collaboration and data sharing by allowing users to share queries, templates, results, and reports across project teams, campuses, and other organizational units. Chemical intelligence, performance, and analytical sophistication lie at the heart of the new system, which was developed entirely in-house. ABCD is used routinely by more than 1000 scientists around the world and is rapidly expanding into other functional areas within the J&J organization.

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     Corresponding author phone:  (610) 458-6045; fax:  (610) 458-8249; e-mail:  [email protected].

     Exton, PA.

     La Jolla, CA.


     Beerse, Belgium.

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    53. Josef Scheiber. How can we enable drug discovery informatics for personalized healthcare?. Expert Opinion on Drug Discovery 2011, 6 (3) , 219-224.
    54. Robert C Glen. Connecting the virtual world of computers to the real world of medicinal chemistry. Future Medicinal Chemistry 2011, 3 (4) , 399-403.
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