Chemical structure handling systems

For Version 2 of ABACUS we needed a chemical structure handling system to add the following facilities to ABACUS. 

The universal interface is thus an exciting objective, but, related to it, and equally important, is the need for standards which allow the transfer of data between many different chemical structure handling systems. 

Most large companies are developing office automation systems, as an adjunct to their word processing capability, using local area networks for electronic mail. If they have a need for chemical structure handling within those facilities, in other words if they have chemical documents or reports which they want to send through an electronic mail system, the standard facility should be used and the chemical application software should fit within the standard facility. 

A chemical information system, in a chemical or pharmaceutical company requires access to 2 different types of data the chemical structures handled by a chemical data base system and the information related to chemical structures including biological activity and toxicology handled by a data base management system (DBMS). 

The CALL facility allows the expert system to access software external to the LISP program. Included with the CALL is the name of a LISP function which handles the outside software. In the case of the fact CHEMICAL NAME, the LISP function executes a FORTRAN program which allows the user to either retrieve the structure of a previously entered compound or enter a new one. The program also breaks the chemical structure into its functional groups. When the FORTRAN program terminates, the LISP function updates the list of facts, and inserts the name into CHEMICAL NAME and the functional groups into FUNCT GROUPS. These FACTS are then available to the expert system. In this way, access to outside software is completely data driven. 

Fig. 9.3 Flowchart illustrating how data is automatically handled and processed to yield the chemical structure of a hit. The LC/MS systems have been integrated with software to automatically deconvolute each protein charge state distribution and determine potential protein conjugation and obtain the structure of a hit by database searching.

MAECIS contains five major sections that are integrated into a single system. At its center is a database management system that handles the storage and updating of data and chemical structures. Associated with this section is an information retrieval section that allows one to search the database for specific information composed of any combination of data and/or substructures. Once information is retrieved, it can be displayed on a computer terminal or sent to a printer for hardcopy output using the display section of MAECIS which includes the ability to display chemical structures in various formats. The final two sections of MAECIS allow for the manipulation of chemical structures and the calculation of various molecular properties that are related to chemical structures. 

As such, any chemical registration system should be structure centric. It must assist the user to get the structure right—make sure the structure is compliant with all business conventions and salts are added correctly and charge balanced. The whole process of structure handling must be optimized to be as efficient, fast, and accurate as possible. 

Jim Downs (1992) of Eastman Chemical Company has insightfully pointed out the importance of looking at the chemical component balances around the entire plant and checking to see that the control structure handles these component balances effectively. The concepts of overall component balances go back to our first course in chemical engineering, where we learned how to apply mass and energy balances to any system, microscopic or macroscopic. We did these balances for individual unit operations, for sections of a plant, and for entire processes. 

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