Molecular registration systems

Appendix 1 Drug, MOLECULAR REGISTRATION Systems, AND CHEMISTRY DATA Cartridges... 

Some systems support various structure formats and need to convert the structures from one format to another from time to time. Although this may not be required by a registration system, it could be very useful in other types of chemical information systems such as molecular modeling. The good news is that some tools from the major chemical informatics software vendors can do the conversions. In this situation, commercial solutions make sense because you do not want to reinvent the wheel. 

One critical task of any compound registration system is to make sure molecular structures are compliant with chemistry conventions. This ensures consistent representations of molecular structures in the database so that structure searches can find, and only find, the right compounds. Although different organizations may have slightly different conventions, the following ones are some of the most common that the Chemistry Intelligence API takes care of. 

Chemists talk to each other by drawing pictures, and when nearly two decades ago software became readily available that allowed this to be done electronically, the office environment for chemists changed in a remarkable manner. Well established commercial office packages allow even the most complicated chemical structures to be drawn easily and incorporated into word processing software to use electronic notebooks (see Section B, 3.3.2.6) access databases both external and internally on CD-ROMs integrate into a LIMS use a registration system carry out molecular modelling and determine structure activity relationships [B-ll]. 

Figure 9.3. MACCS— the Molecular ACCess System—an early structure indexing system. This program originally used fixed menus for searching, registration, and reporting. Later versions allowed users to customize the menus. The figure shows the result of a 3D pharmacophore search for ACE inhibitors. Out of a database of 115,000 structures, 21 fit the 2D and 3D requirements of the search query. The user could typically browse the "hits" from the search, save the list of structures to a list file, and output the structures to a structure-data file (SDFile). The MACCS database was a proprietary flat database system in which data of a given type, say, formula, was stored in a given file, indexed by the compound ID number.

White et al. [53] reported open-access LC-MS cf. Ch. 9.2) for the rapid characterization of proteins. The system allows web-based sample submission and registration, automated data processing, interpretation, and report generation. The submitted amino-acid sequence is used to set parameters for the transformation of the mass spectmm into the protein molecular weight and to evaluate whether the submitted protein is actually detected. Data acquisition is performed on a TOF instrument in order to achieve sufficient mass accuracy. 

CAS = Chemical Abstracts Service CSD = Cambridge Stmctural Database CT = connection table DBMS = database management system MDL = Molecular Design Ltd. RN = registration number, RTECS=Registry of Toxic Effects... 

Figure 13 represents a chemical structure record as It Is Input to the system. The L-number In the upper left Is the registration number. This Is followed by the molecular formula, then any stereo descriptors, reference to source, and finally the chemical structure. This Is a typical single record. The file contains approximately 135,000 such records. The year of registration Is added to the record automatically at the time of Its Input to the system. 

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