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      marvin: A Platform for Chemoinformatics Software Development

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          Abstract

          A strategy for a new type of platform for chemoinformatics software development and its first implementation are presented. The basic task of such a platform is to apply sequences of computational methods to high numbers of molecules. The implementation presented is based on four major components: (a) the application manager, responsible for running programs and for data management; (b) executable applications that supply limited pieces of functionality; (c) syntax definitions for data and control files and (d) the runtime library which comprises routines for data handling and user interface. This simple concept is implemented in the software package marvin . Different computational methods are available within marvin , including parts of commercial software packages (e.g. molecular modeling, bioinformatics, statistics, etc.) as well as newly developed and innovative algorithms. The basic layout of marvin is described and a simple example illustrates its application.

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          Most cited references25

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          Target-oriented and diversity-oriented organic synthesis in drug discovery.

          Modern drug discovery often involves screening small molecules for their ability to bind to a preselected protein target. Target-oriented syntheses of these small molecules, individually or as collections (focused libraries), can be planned effectively with retrosynthetic analysis. Drug discovery can also involve screening small molecules for their ability to modulate a biological pathway in cells or organisms, without regard for any particular protein target. This process is likely to benefit in the future from an evolving forward analysis of synthetic pathways, used in diversity-oriented synthesis, that leads to structurally complex and diverse small molecules. One goal of diversity-oriented syntheses is to synthesize efficiently a collection of small molecules capable of perturbing any disease-related biological pathway, leading eventually to the identification of therapeutic protein targets capable of being modulated by small molecules. Several synthetic planning principles for diversity-oriented synthesis and their role in the drug discovery process are presented in this review.
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            High-throughput screening: new technology for the 21st century.

            New technologies in high-throughput screening have significantly increased throughput and reduced assay volumes. Key advances over the past few years include new fluorescence methods, detection platforms and liquid-handling technologies. Screening 100,000 samples per day in miniaturized assay volumes will soon become routine. Furthermore, new technologies are now being applied to information-rich cell-based assays, and this is beginning to remove one of the key bottlenecks downstream from primary screening.
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              Computational methods for the prediction of 'drug-likeness'

              Recently, one of the key trends in the pharmaceutical industry has been the integration of what have traditionally been considered 'development' activities into the early phases of drug discovery. The aim of this paradigm shift is the prompt identification and elimination of candidate molecules that are unlikely to survive later stages of discovery and development. In this review, the authors examine the growing role that is being played by computational methods in this filtering process, with a particular focus on the prediction of intestinal absorption and blood-brain barrier penetration.
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                Author and article information

                Journal
                Molecules
                Molecules
                molecules
                Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry
                MDPI
                1420-3049
                28 February 2002
                February 2002
                : 7
                : 2
                : 206-238
                Affiliations
                Institute of Pharmaceutical Chemistry, University of Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen , Germany.
                Author notes
                [* ] Author to whom correspondence should be addressed. Current address: Byk Gulden, Byk-Gulden-Straße 2, D-78467 Konstanz, Germany; E-Mail: andreas.dominik@ 123456byk.de
                Article
                molecules-07-00206
                10.3390/70200206
                6146780
                1f94f330-ff4e-4ac7-ab57-34abedf63d29
                © 2002 by MDPI (http://www.mdpi.org).

                Reproduction is permitted for non commercial purposes.

                History
                : 11 October 2001
                : 26 February 2002
                : 26 February 2002
                Categories
                Article

                chemoinformatics,software platform,chemical similarity assessment,data management,drug discovery

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