title: FOCUS--Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists.
abstract: Communication of data and ideas within a medicinal chemistry project on a global as well as local level is a crucial aspect in the drug design cycle. Over a time frame of eight years, we built and optimized FOCUS, a platform to produce, visualize, and share information on various aspects of a drug discovery project such as cheminformatics, data analysis, structural information, and design. FOCUS is tightly integrated with internal services that involve-among others-data retrieval systems and in-silico models and provides easy access to automated modeling procedures such as pharmacophore searches, R-group analysis, and similarity searches. In addition, an interactive 3D editor was developed to assist users in the generation and docking of close analogues of a known lead. In this paper, we will specifically concentrate on issues we faced during development, deployment, and maintenance of the software and how we continually adapted the software in order to improve usability. We will provide usage examples to highlight the functionality as well as limitations of FOCUS at the various stages of the development process. We aim to make the discussion as independent of the software platform as possible, so that our experiences can be of more general value to the drug discovery community.
authors: †Novartis Institute for Biomedical Research, Postfach, CH-4002 Basel, Switzerland.
authors: Nikolaus
authors: N
authors: Stiefl
authors: ‡Novartis Institute for Tropical Diseases Pte. Ltd., 10 Biopolis Road, #05-01 Chromos, Singapore 138670.
authors: Peter
authors: P
authors: Gedeck
authors: §Novartis Institute for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.
authors: Donovan
authors: D
authors: Chin
authors: ∥Novartis Institute for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, United Kingdom.
authors: Peter
authors: P
authors: Hunt
authors: ⊥Novartis Institute for Biomedical Research, 4560 Horton Street, Bldg. 4, Emeryville, California 94608, United States.
authors: Mika
authors: M
authors: Lindvall
authors: ∥Novartis Institute for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, United Kingdom.
authors: Katrin
authors: K
authors: Spiegel
authors: §Novartis Institute for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.
authors: Clayton
authors: C
authors: Springer
authors: §Novartis Institute for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.
authors: Scott
authors: S
authors: Biller
authors: #Novartis Institute for Biomedical Research, 11/2 Muthgasse, 1190 Wien, Austria.
authors: Christoph
authors: C
authors: Buenemann
authors: ∇Novartis Institutes for BioMedical Research, Ohkubo 8, Tsukuba, Ibaraki 300-2611, Japan.
authors: Takanori
authors: T
authors: Kanazawa
authors: §Novartis Institute for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.|∇Novartis Institutes for BioMedical Research, Ohkubo 8, Tsukuba, Ibaraki 300-2611, Japan.
authors: Mitsunori
authors: M
authors: Kato
authors: †Novartis Institute for Biomedical Research, Postfach, CH-4002 Basel, Switzerland.
authors: Richard
authors: R
authors: Lewis
authors: ⊥Novartis Institute for Biomedical Research, 4560 Horton Street, Bldg. 4, Emeryville, California 94608, United States.
authors: Eric
authors: E
authors: Martin
authors: ⊥Novartis Institute for Biomedical Research, 4560 Horton Street, Bldg. 4, Emeryville, California 94608, United States.
authors: Valery
authors: V
authors: Polyakov
authors: §Novartis Institute for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.
authors: Ruben
authors: R
authors: Tommasi
authors: §Novartis Institute for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.
authors: John
authors: J
authors: van Drie
authors: §Novartis Institute for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.
authors: Brian
authors: B
authors: Vash
authors: §Novartis Institute for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.
authors: Lewis
authors: L
authors: Whitehead
authors: ⊥Novartis Institute for Biomedical Research, 4560 Horton Street, Bldg. 4, Emeryville, California 94608, United States.
authors: Yongjin
authors: Y
authors: Xu
authors: ○Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, California 92121, United States.
authors: Ruben
authors: R
authors: Abagyan
authors: ○Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, California 92121, United States.
authors: Eugene
authors: E
authors: Raush
authors: ○Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, California 92121, United States.
authors: Max
authors: M
authors: Totrov
mesh_terms: D002626:Chemistry, Pharmaceutical / Q000379:methods*; D003142:Communication; D019295:Computational Biology; D003198:Computer Simulation; D055808:Drug Discovery / Q000379:methods*; D008024:Ligands
chemical_list: D008024:Ligands