From chemistry-request@ccl.net Sun Mar 22 21:01:58 1992 Date: Mon, 23 Mar 92 11:12:10 EST From: Dave Winkler (Dr.) Subject: Responses to MACCS alternative query To: chemistry@ccl.net Status: R Dear Netters, The following is a summary of the responses to my question as to whether there were useful alternatives to the MACCS database. Thank you to all the people who responded so promptly. Dave +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ David Hoekman,Pomona College summarised the work of Dr. Dave Weininger on the development of the SMILES notation and 'Thor' and'Merlin'. Thor is a THesaurus-ORiented database which stores, on a per structure basis, any type of information that you care to store (the fields are user-definable). Merlin is a substructure searching system. The Merlin searching algorithm is efficient; searches are fast, even on older machines Dave Weininger has left Pomona College formed his own company, Daylight Chemical Information Systems. To contact their business office: DAYLIGHT Chemical Information Systems P.O. Box 17821 Irvine, CA USA 92713-7821 (714) 476-0451 phone (714) 476-0645 fax +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Yvonne Martin, Abbott Laboratories gave her experiences with using the Daylight Chemical Information System. It is much superior in handling chemical structures, searches, etc. They store in the database our conformations, measured biological activities, calculated logP's etc. They have a very good similarity searching capability since their structure keys are generated from all substructures in the molecules rather than from pre-assigned ones al la MDL. Recently they added the capability to cluster the whole database based on similarity. Yvonne felt that if you need to do really relational database stuff, then there might be limitations in the Daylight software as currently programmed. It all is MUCH friendlier than MACCS and MUCH faster. There is a VAX version, but the newest is UNIX working on SPARC, ESV, and SG. In addition, there is available a number of toolkits for customized programming. There are two limitations in the current application programs. The first is that handling the associated data is not up to the level of ORACLE. (Ties should be pretty easy using the toolkit I expect). The second is that the hard-copy is not really there in terms of a report-writer. It is more for a sophisticateduser except for screen dumps. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ George R Famini recommended a PC based product, ISIS Base from MDL (again, (*sigh*)). ISIS is a significant improvement over Chembase (no comparison). +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Stephen R. Heller suggested a a new compnay, BioCAD which is said to have software which they claim to be competitive with MDL systems. They are to have a booth at the ACS meeting next month in San Francisco. Their address/phone FAX number is: BioCAD 1390 Shorebird Way Mountain View, CA 94043 415-903-3900 / FAX: 961-0584 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Jim Bentley, Burroughs Wellcome Co , also suggested software from Daylight Chemical Information Systems, Inc. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Thomas Pierce, Rohm and Haas, suggested contacting Dan Chodosh at Distributed Chemical Graphics (215)-355-2365 or fax (215)-355-0954. His company has a workstation based solution called SYNLIB. It's pretty nice. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Eve Zoebisch, SRI International, also recommended DAYLIGHT Chemical Information Systems, Inc. Unfortunately it is not integrated to a relational database, however our database engineers tell us it would not be difficult todo (given the right relational database). A few of the database software companies have developed a user defined variable type (otherwise known as an abstract variable type) and an open server which would be necessary forthis application. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dennis Gerson, IBM Technical Computing Systems, noted that it all comes down to how much money you are willing to spend. Daylite Software sell database tools which utilize SMILES format to link a drawing package, such as CHEMDRAW, with a structured database,THOR, to create a system. You have to do all the programming to make it work. Tripos and Chemical Design Ltd(UK) have 3D database products which compete with MACCS-3D but require you to create the actual data for the databases. Finally, CAS (Chemical Abstracts System) licenses their inhouse system to customers. __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia.