Molecular Design Limited System

Parallel to that the MDL Molfile format (see the Tutorial in Section 2.4.6) developed at Molecular Design Limited (now MDL Information Systems, Inc.) became a de facto standard file format [50]. 

MACCS/ISIS Databases and DB management systems Daylight Chemical Infor-mation Systems Molecular Design Limited, Inc. (MDLI)... 

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. 

Molecular Design Limited (MDL) has marketed an Integrated Scientific Information System tlSISt. which provides the capability to query multiple systems, including binary, text, proprietary, and relational databases across glohal networks, thereby providing transparent deskiop access to multiple autonomous data sources. 

To cover the specialized area of chemical structures in detail, authors could provide only cursory coverage of mathematical expressions and tabular material. Many of the scientific word processing packages that I mentioned and some software the book discusses in detail (especially ChemText from Molecular Design Limited) will handle scientific and graphics material other than chemical structures. This book does not cover well-known graphics systems that handle chemical structures or chemical reactions these systems are already well-documented (6, 7). 

The next step up in integration places as much information as possible in the chemical structure or reaction DBMS. For example, Molecular Design Limited s MACCS system has been used to store structures, reactions, biology, spectra, inventory, and document index information. This approach provides a good degree of data integration but suffers from poor performance for large databases. Additionally, the retrieval capabilities of the structure DBMS are inadequate for certain types of information. 

ChemText - Microcomputer chemical information system and chemical word processor, hardware supported IBM PC, available from Molecular Design Limited, 2132 Farallon Drive, San Leandro, CA 94577, U.S.A. 

At this point only two alternatives remained MACCS from Molecular Design Limited (MDL) and enhancing CSIS. A comprehensive study by the Corporate computer support group concluded that 36 man-months were needed to complete the work begun in 1982, to enhance CSIS to an online interactive system. MSDRL management felt that a commercial system would be able to meet the scientists needs in much less time. Also there were only a few IBM compatible terminals in MSDRL, in contrast to the many VAX compatible terminals. Acquiring more IBM terminals presented an additional cost factor to enhancing CSIS. The decision was made to drop CSIS from further consideration. 

The major commercially available reaction indexing programs are REACCS (Molecular Design Limited), SYNLIB (started by Clark Still, developed by Smith, Kline and French and now sold by Dan Chodosh), ORAC (developed at the University of Leeds) and DARC-RMS (Telelsystemes). Pfizer s in-house system CONTRAST is noteworthy but is not available outside Pfizer. The release of CASREACT by Chemical Abstracts is awaited with interest. 

REACCS, the reaction management system developed by Molecular Design Limited, effectively handles information on reactions as well as on molecules. The use of this program in environments as different as laboratories in basic research or process... 

Fig. 2.12 Molecular Design Limited Molecular ACCess System (MACCS) fingerprints computed for Ames data set...

Molecular Design Limited has recently extended their MACCS-II chemical database system to MACCS-3D, for the storage and retrieval of three-dimensional atomic coordinates. Physical and biological data may be stored. A novel feature of MACCS-3D is the ability to recognize and remove duplicate coordinate sets. Coordinate sets can be retrieved from the database by specifying a combination of numerical and textual queries or by substructure. 

Since 1986, others have developed their own speciaUsed 3-D searching systems. These systems include the ALADDIN system developed at Abbott, the 3DSEARCH system developed at Lederle, and the MACCS-3D system developed by Molecular Design Limited in collaboration with an industrial consortium. Any one of these systems can be used to develop synthetic targets using the strategy outlined above. 

MM3 calculations were carried out with a MM3 ( 92) program in its ANCHOR II implementation. ANCHOR II is a molecular design support system for SUN computers from Fujitsu Limited. Trade Mark of Fujitsu Limited and Kureha Chemical Company, 1992. In these calculations, the memory size of the hardware was limited, thus, molecules larger than p-diisopropyldihomoazacalix[4]arene were not considered for the model. 

CAS = Chemical Abstracts Service CIP = Cahn-Ingold-Prelog system of labeling stereogenic atoms and bonds MDLI = Molecular Design Limited, Inc. MIF = molecular information file MOLFile = molecule file SEMA = stereo-chemically extended Morgan algorithm SMD = Standard Molecular Data SMILES = simplified molecular input line entry specification. 

Once many in-house, chemical structure data bases had been built, the users began to realize that it was more efficient to use commercially-available structure handling software for structures alone (or structures and a minimal amount of related property data) and to take advantage of data base management systems to handle property data. Molecular Design Limited (MDL) and Telesystemes modified their MACCS and DARC software, respectively, to allow for the appropriate interfacing of structures and data. 

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