Medicinal chemistry databases

A method to identify common scaffolds in databases by scaffold detection, alignment, and assignment has been reported [58]. This method could be used to create meaningful SAR analyses of large medicinal chemistry databases. 

The Comprehensive Medicinal Chemistry database is available from MDL Information Systems, Inc., http //www.mdli.com/products/ knowledge/medicinaLchem/index.jsp. 

Comprehensive Medicinal Chemistry Database, 94.1 Distributed by MDL Information Systems San Leandro, CA. 

Charifson P S, J J Corkery, M A Murcko and W P Walters 1999. Consensus Scoring A Method fc Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures int Proteins. Journal of Medicinal Chemistry 42 5100-5109. 

Currunins D J, C W Andrews, J A Benfley and M Cory 1996. Molecular Diversity in Chemical Database Comparison of Medicinal Chemistry Knowledge Bases and Databases of Commercially Availabl Compounds Journal of Chemical Information and Computer Science 36 750-763. 

DJ Cummins, CW Andrews, JA Bentley, M Cory. Molecular diversity m chemical databases Comparison of medicinal chemistry knowledge bases and databases of commercially available compounds. I Chem Inf Comput Sci 36 750-763, 1996. 

Web in the life of the medicinal chemist. One may see the development of alerting services for the primary medicinal chemistry journals. The Web-based information search process could be replaced by a much more structured one based on metadata, derived by automated processing of the original full-text article. To discover new and potentially interesting articles, the user subscribes to the RSS feeds of relevant publishers and can simply search the latest items that appear automatically for keywords of interest. The article download is still necessary, but it may be possible for the client software to automatically invoke bibliographic tools to store the found references. Another application of the Chemical Semantic Web may be as alerting services for new additions to chemical databases where users get alerts for the new additions of structures or reactions. 

P. W., Hoffman, R. Catalyst pharmacophore models and their utility as queries for searching 3D databases. In Computer-Assisted Lead Finding and Optimization - Current Tools for Medicinal Chemistry, Van de Waterbeemd, H., Testa, B Folkers, G. (eds.),VHCA, Basel, 1990,... 

Ghose, A. K, Viswanadhan, V. N., Wendoloski, J. J., A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases, J. Comb. Chem. 1999,... 

While not convincing from a statishcal perspective, the results in this section are consistent with a trend high-activity molecules published in the past decade of medicinal chemistry literature are more likely to be found in the large, hydrophobic and poor solubility corner of chemical property space. These results are not consistent with, for example, cell-based [41] and median-based [42] partihoning of biologically active compounds however, such analyses were performed in the presence of inactive compounds selected from MDDR[41] or ACD [42], with quite probably unrelated chemotypes. ACD, the Available Chemicals Directory [43], and MDDR, the MDL Drug Data Report [43], are databases commonly used by the pharmaceuhcal industry. 

The examples from SciFinder and the Merck Index are not intended to question the quality of these products, which we consider to be outstanding. They are invaluable resources to many chemists worldwide, and the error rate in these two databases is insignificant if one takes into account the enormous volume of indexed data. One of us has published a structure-activity paper on HIV-protease inhibitors [31] where a modified peptide was present in both the training set and the test set. Al Leo of Pomona College has recently [32] detected 100 chemical and name errors in the printed version of the sixth edition of Burger s Medicinal Chemistry [33], errors that will be corrected in the on-line edition [34]. One can never be too careful in verifying the available information, in particular if one is to invest a significant amount of resources in that area. 

WOMBAT [39] is a Cabinet database that provides information about biological activity of small molecules [40]. The dataset comes from publications in the Journal of Medicinal Chemistry and other periodicals. WOMBAT is updated twice a year. The data consist of series of compounds that were observed and compared for a specific activity, for example, Ki, IC50, D2 and EC50. The database also includes calculated LogP and Log S values, as well as other descriptors related to flexibility, size, and so on. 

Most prediction tools for druglikeness use the MDL Available Chemicals Directory (ACD) [89] as a list of nondrugs and one of three databases as a list of drugs MDL Drug Data Report (MDDR) [89], MDL Comprehensive Medicinal Chemistry (CMC) [89], or Derwent World Drug Index (WDI) [90]. 

MDDR is a database derived principally from the patent literature, journals, and meetings. It contains the structures of approximately 130000 compounds of which approximately 1000 are launched drugs. WDI is a Derwent database of approximately 73 000 marketed drugs and development compounds, drawn from journals, scientific meetings, and approved name lists. CMC is a list of about 8400 compounds taken from the Drug Compendium in Pergamon s Comprehensive Medicinal Chemistry [94] and also from the United States Approved Names list. 

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