Responses to MACCS alternative query
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.