MDL databases

This review includes most of the published articles from the defined area and excludes only imidazoquinolines, which were reviewed in Weissberger-Taylor s series The Chemistry of Heterocyclic Compounds (81MI1). Comprehensive Heterocyclic Chemistry II (96MI1) mentioned only some of the azoloquinolines in the first edition the authors omitted citations about this type of compounds. The trend toward interest in these compounds can be illustrated by the number of citations in Chemical Abstract as shown in Table I. Besides Chemical Abstracts Substance/Subject (Collective) Indexes, the MDL database search has been used. 

Readers who are familiar with the MDL database should not be surprised to see MDL s structure query operators such as sss, molsim, and flexmatch. The CompoundMapper s StatementSource objects use ChemDBQueryBuilder to append these structure search operators to the structure search SQL statements. Take the substructure search as an example. In CompoundMapper, we have an inner class FindBySubstructure whose getSql() method is as follows ... 

Fastsearch Index. Term used in MDL databases for a tree-structured index of all the structures in the database. The nodes in the tree represent increasingly complex substructures or properties, where all the structures at or below a given node have in common. The fastsearch index can be very large, but it makes possible very rapid substructure searching. 

Available Chemicals Directory MDL database Is a chemical database providing access to pricing and supplier information for more than 400,000 research-grade and bulk chemicals. Available at http //www.mdl.com. Accessed March 28. 2007. 

Retrieval of Polymer Structures, it is axiomatic that to conduct an efficient search, searchers need to know the rules of the database or file being searched. Although this article is not intended to be a teaching manual on how to search polymer files or databases, some basic differences between searching the CAS Registry File and searching an MDL database by means of the ISIS program merit discussion. 

The most important Plug-In for chemistry is Chime from MDL Information Sy.stems. Chime contains all the functionality of rasmol plus 2D-display features and extended script-ability for animations. A professional version which interfaces to MDL databases is also available. Chime is available for IRIX, PC, and Macintosh platforms, but not for anything else. Chime applications are described in Internet-based Computational Chemistry Tools. 

Sf The Chemlnjbrm RX reaction database is produced by FIZ Chemie, Berlin, Germany, and marketed by MDL Information Systems, Inc., San Leandro, CA, USA. 

More than 10 000 databases exist that provide a small or large amount of data on various topics (including chemistry). The contents in databases are supplied by approximately 3500 database developers (e.g., the Chemical Abstracts Service, MDL Information Systems, etc.). Since there is a variety of topics from economics to science, as well as a variety of structures of the database, only some of the vendors (-2000) offer one or more databases as either local or as online databases (Figure 5-4) [4]. Usually, databases are provided by hosts that permit direct access to more than one database. The search occurs primarily through different individual soft-... 

The database is produced by the German Chemical Society (GDCh) and provided by MDL Information Systems Inc. [22]. 

This tutorial describes briefly some of the search capabilities possible with Cheminform RX and MDL" ISIS used as the retrieval system. In this tutorial, the CIRX database. of the years 1992-1996 arc used, containing altogether 334 855 reactions. 

P2] More Information about this database is available at the MDL websites http // uww.mdli.comj... 

MDL Information Systems, Inc. MDL provides modular software systems for managing chemical information, as weU as related molecular and reaction databases for use with the software. MDL s database management programs, MACCS-II and REACCS, provide access to compound and reaction databases and also have the capabiHty to manage user-created databases (37). Although MDL is not considered to be an on-line database vendor, it is mentioned here because of the value of its information products and services to the chemical industry. 

Nuclear Magnetic Resonance Spectroscopy. Bmker s database, designed for use with its spectrophotometers, contains 20,000 C-nmr and H-nmr, as weU as a combined nmr-ms database (66). Sadder Laboratories markets a PC-based system that can search its coUection of 30,000 C-nmr spectra by substmcture as weU as by peak assignments and by fiiU spectmm (64). Other databases include one by Varian and a CD-ROM system containing polymer spectra produced by Tsukuba University, Japan. CSEARCH, a system developed at the University of Vieima by Robien, searches a database of almost 16,000 C-nmr. Molecular Design Limited (MDL) has adapted the Robien database to be searched in the MACCS and ISIS graphical display and search environment (63). Projects are under way to link the MDL system with the Sadder Hbrary and its unique search capabiHties. 

All chemical shift data presented in this book come either from the primary literature or from spectra obtained in the author s laboratory. All spectra actually depicted in the book derive from spectra obtained by the author at the University of Florida. All data from the literature were obtained via searches using MDL Crossfire Commander or SciFinder Scholar. Persons interested in accessing such primary literature can do so readily via these databases by simply searching for the specific compound mentioned in the text. 

Regarding the multitude of NMR chemical shifts of specific compounds that are provided within the text, references for chemical shifts of individual compounds for the most part will not be cited. It is assumed that if such references are required, the reader can find them by a quick search using either MDL Crossfire Commander or SciFinder Scholar. The author found MDL Crossfire Commander the superior database for locating specific NMR data. 

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. 

MDDR and ACD are available from MDL Information Systems, http //www.mdli.com/products/finders/ database.finder/ MDDR is developed in cooperation with Prous Science Publishers, 2004,... 

Interestingly, the PRCC is relatively free of compounds that violate Lipinski s Rule of Five (ROF) [15] as shown in Table 13.1. Similar ROF behavior has also been observed by Oprea [16] for other compound databases including the ACD and the MDDR (MDL Drug Data Report, MDL Information Systems, San Leandro, CA). 

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