An Integrated Data Management Framework for Drug Discovery – From Data Capturing to Decision Support

Abstract

Drug discovery is a highly complex process requiring scientists from wide-ranging disciplines to work together in a well-coordinated and streamlined fashion. While the process can be compartmentalized into well-defined functional domains, the success of the entire enterprise rests on the ability to exchange data conveniently between these domains, and integrate it in meaningful ways to support the design, execution and interpretation of experiments aimed at optimizing the efficacy and safety of new drugs. This, in turn, requires information management systems that can support many different types of scientific technologies generating data of imposing complexity, diversity and volume. Here, we describe the key components of our Advanced Biological and Chemical Discovery (ABCD), a software platform designed at Johnson & Johnson to bring coherence in the way discovery data is collected, annotated, organized, integrated, mined and visualized. Unlike the Gordian knot of one-off solutions built to serve a single purpose for a single set of users that one typically encounters in the pharmaceutical industry, we sought to develop a framework that could be extended and leveraged across different application domains, and offer a consistent user experience marked by superior performance and usability. In this work, several major components of ABCD are highlighted, ranging from operational subsystems for managing reagents, reactions, compounds, and assays, to advanced data mining and visualization tools for SAR analysis and interpretation. All these capabilities are delivered through a common application front-end called Third Dimension Explorer (3DX), a modular, multifunctional and extensible platform designed to be the "Swiss-army knife" of the discovery scientist.

Assessment of the Fragment Docking Program SEED

“…The protein sequences were first aligned and superimposed, and the RMSD was measured over all backbone atoms for the full protein and for all heavy atoms of residues within 4.5 Å of either ligand (Table S2). The number of rotatable bonds of the fragments was calculated using the Janssen in-house Third Dimension Explorer (3DX) tool . Fragment charges were calculated using MOE.…”

“…The number of rotatable bonds of the fragments was calculated using the Janssen in-house Third Dimension Explorer (3DX) tool. 44 Fragment charges were calculated using MOE.…”

Modeling Complex Metabolic Reactions, Ecological Systems, and Financial and Legal Networks with MIANN Models Based on Markov-Wiener Node Descriptors

“…Prado-Prado and García-Mera have also guest-edited a special issue about computer-aided drug design and molecular docking for disorders of the central nervous system and other diseases . González-Díaz has guest-edited two special issues about multitarget models and Complex Networks applied to medicinal chemistry. , In all these issues, and others of the same journal, several review and research papers in this area ,,− have been published.…”