From szilagyi-: at :-indy.mars.vein.hu Tue Jan 3 10:44:17 1995 Received: from miat0.vein.hu for szilagyi -x- at -x- indy.mars.vein.hu by www.ccl.net (8.6.9/930601.1506) id KAA05305; Tue, 3 Jan 1995 10:10:32 -0500 Received: by miat0.vein.hu (5.65/DEC-Ultrix/4.3) id AA04016; Mon, 2 Jan 1995 11:12:31 -0600 Received: by indy.mars.vein.hu (931110.SGI/930416.SGI.AUTO) for -: at :-miat0.vein.hu:chemistry-: at :-ccl.net id AA01059; Mon, 2 Jan 95 11:16:12 +0100 From: "Robert K. Szilagyi" Message-Id: <9501021116.ZM1057 -AatT- indy.mars.vein.hu> Date: Mon, 2 Jan 1995 11:16:05 +0100 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry()at()ccl.net Subject: Synthesis desing and databases Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear Fellows, first of all, I would like to wish a happy and cheerful New Year to everyone on this list! As a matter of fact, I promised still in 1994 to give a summary about the synthesis planning expert systems. Here you are! Thanks again to everyone for helping me to get the taste of this topic. As it comes from the following messages, the LHASA, CAMEO and CHIRON are the most favourable softwares. Please, let me know if there is anything else! THE SUMMARY ******************************************************************************** >From dimitris "-at-" 3dp.com Tue Nov 29 19:41:34 1994 There are a few around, but the most advanced is LHASA (Logic and Heuristics Applied to Synthetic Analysis) out of EJ Corey's group at Harvard. For more information, contact: Dr. Alan Long Director Department of Chemistry Harvard University 12 Oxford Street Cambridge, MA 02138 tel: (617) 495-4283 e-mail: long (- at -) chemistry.harvard.edu. or EJ himself at the same address. Please let me know if you need more information or can't get through to Alan. Dimitris K. Agrafiotis, PhD | e-mail: dimitris(-(at)-)3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 ******************************************************************************** >From BRIGGS # - at - # kitten.chem.uh.edu Tue Nov 29 19:49:14 1994 Rob, Check out CAMEO (Computer Assisted Mechanistic Evaluation of Organic Reactions) from the Jorgensen group at Yale. CAMEO predicts plausable results of an organic reaction based on the starting materials and conditions. The algorithms used in CAMEO are based on mechanistic rules/trends derived from the literature (i.e. NOT database driven). Prof. Jorgensen can be reached at: bill %-% at %-% doctor.chem.yale.edu Jim Briggs ******************************************************************************** >From MARTIN%cmda - at - randb.abbott.com Tue Nov 29 20:00:16 1994 You might be able to get Chiron from Stephen Hanessian at the University of Montreal. I think the price is nominal. Email hanessia ^at^ ere.umontreal.ca. Yvonne Martin Abbott Laboratories ******************************************************************************** >From eduffy-: at :-laplace.csb.yale.edu Tue Nov 29 21:56:37 1994 A portion of Bill Jorgensen's group at Yale develops CAMEO (Computer Assisted Mechanistic Evaluation of Organic Reactions). They may be reached through Bill: bill -AatT- adrik.chem.yale.edu. In addition, here is the lead reference: Jorgensen, W.L.; Laird, E.R.; Gushurst, A.J.; Fleisher, J.M.; Gothe, S.A.; Helson, H.E.; Paderes, G.D.; Sinclair, S. "CAMEO: a program for the logical prediction of the products of chemical reactions." Pure & Appl. Chem. (1990) v.62, 1921-1932. ******************************************************************************** >From Harold_Helson -x- at -x- camsci.com Wed Nov 30 16:15:47 1994 Another program is CAMEO, on which I worked as a graduate student. It operates in the forward (as opposed to retrosynthetic) direction, predicting the products of organic reactions given starting materials and conditions. For further information contact Professor William Jorgensen at bill at.at adrik.chem. yale.edu. Harold Helson ******************************************************************************** >From blurock()at()risc.uni-linz.ac.at Wed Nov 30 18:02:02 1994 In response to your inquiry about synthesis design programs, I could mention the system developed here. It is described in the paper: J. Chem. Inf. Comp. Sci. 30, pg 505 (1990) Computer-Aided Synthesis Design at RISC-Linz: Automatic Extraction and Use of Reaction Classes I plan to release it to public domain eventually. It runs in COMMON LISP under CLX (an X-window interface for LISP - public domain). At the moment it is a bare-bones system with no database. Part of the work toward releasing it to public domain will be building up (through its analysis techniques) a rudimentary database. It is still in its infancy in regards to 'real' organic reaction searches (This is mainly due to the database), but all the mechanisms are there (with room for improvement). I would be interested to know in more detail your intentions. This is partly for the pragmatic reason that I am only able to work on it in my sparse 'spare time' (thus progress towards public domain is still months away) and would be seriously interested in cooperations in reactivating the system (it has been dormant for a couple of years). Edward S. Blurock ******************************************************************************** >From larouche &$at$& ERE.UMontreal.CA Wed Nov 30 19:50:57 1994 Here are some information about computer programs out of S. Hanessian's group at Universite de Montreal. For more information, please send email to hanessia %! at !% ere.umontreal.ca The Chiron Program (version 4.22) --------------------------------- The Chiron Computer Program is an interactive program for the analysis and perception of stereochemical features in molecules and for the selection of chiral precursors in organic synthesis. It features Computer Assisted Stereochemical Analysis (CASA), and Computer Assisted Precursor Selection (CAPS). CASA is concerned with the recognition of stereochemical and symmetry elements in a molecule. CAPS probes the structure in question and suggest appropriate precursors from a data base of 4567 chiral and achiral molecules. The Chiron program also has 3-D graphics capability and interfaces with sybyl, macromodel, reaccs, x-ray data bases, etc. Applications in research (drug design and synthesis, chemical diversity, natural and unnatural product synthesis.) and in teaching. Available on Macintosh, SiliconGraphics and V.A.X. ChemProtect (version 1.0) ----------- ChemProtect is a new software designed to help chemists in the selection of protective groups in synthesis. ChemProtect works on the Apple Macintosh. It is available in two versions (English and French). A modified version of this software is also available on UNIX (Iris Series) and VAX/VMS. This software contains 346 protective groups and 161 reaction conditions for a total of 55706 possible reactivities. Finally, there are 1413 literature references built in the database. There are general references (reviews, etc.) and specific references to the primary literature. ChemProtect is innovative in many ways since the interface is interactive, intuitive and very easy to use. It has three search options: Compatibility, Deprotection and Incompatibility. - The Compatibility search allows you to find all protective groups for selected chemical functions that will be stable to 1 up to 10 reaction steps simultaneously. - The Incompatibility search allows you to look for conditions that modify selected protective groups (up to 10 also). - The Deprotection search allows you to look for conditions that selectively deprotect a set of protective groups up to 10 at the same time. Benoit Larouche Agent de Recherche | INTERNET : larouche &$at$& chimcn.umontreal.ca Departement de Chimie | larouche()at()ere.umontreal.ca Universite de Montreal | TELEPHONE: (514) 343-6111 x3969 ******************************************************************************** Rob, You recently requested via CCL information regarding "expert systems in synthesis design". I have pleasure in enclosing information about LHASA, which in my opinion is the most sophisticated retrosynthetic analysis program available. If you require further information you may contact me or probably more approriately Al Long. Regards, Craig A. Marby, Ph.D. __o _ \<,_ C.A. Marby marby #*at*# lhasa.harvard.edu (_)/ (_) +1 617 495 2654 (work) ~~~~~~~~~~ +1 617 482 3962 (home, not 24hrs) The LHASA Program The computer program LHASA (an acronym for Logic and Heuristics Applied to Synthetic Analysis), which has been under continuous development at Harvard and various collaborating universities for more than 20 years, is intended to assist organic chemists in designing multistep routes to complex molecules. The program accepts as input a target molecule drawn in the language of structural formulae that is common to all organic chemists. A perception of the target is conducted to identify molecular features that influence the development of retrosynthetic routes (e.g. functional groups, stereocenters, rings, etc.) The user is then prompted to specify a strategy and substrategy, or tactic, to guide the retrosynthetic analysis. Finally, the program selects retroreactions ("transforms") from its chemical knowledge base in accordance with the processing tactic and applies these transforms to generate retrosynthetic precursors which are structurally simpler than the target. The user selects one of the precursors for further processing, and the analysis proceeds in an interactive fashion until readily available hypothetical starting materials are obtained. Graphical Interface The concept of communicating chemical structural information graphically to a computer originated with the DEC PDP-1 version of LHASA (called OCSS) in the late 1960's. This early effort used graphical displays on three CRT's simultaneously, allowing coordinated viewing of a sketching window, a target and precursor display, and a retrosynthetic "tree". The current version of LHASA uses a single CRT, with control passed among several menus. Interaction with the program is entirely graphical, allowing chemists with little or no computer experience to use the program effectively. Considerable effort has been expended in the last few years to enhance the user-friendliness of the program. New features include on-line setup menus for modifying run-time parameters, graphical display of perception information, algorithms for automated selection of strategies and tactics, and on-line explanations of button functions. LHASA supports a variety of monochrome and color graphics devices, including X, the de-facto graphics standard for windowing systems under VMS and Unix. The LHASA program is now supported under VMS (both VAX and Alpha AXP), as well as a number of Unix platforms. Transform Selection and Evaluation The task of choosing the best transforms for retrosynthetic simplification of an arbitrary target structure drawn by the chemist is daunting. The variety of organic structures is enormous, and the number of chemical reactions which could be used to synthesize them is similarly overwhelming. LHASA uses a number of pattern-matching techniques to narrow the search for transforms to a subset of its knowledge base. Some of these techniques are relatively elemental, based only on atoms and the bonds between them, while others rely on convenient "synthetically-significant" structural features such as functional groups, rings, and stereochemical relationships. To further narrow the set of transforms that passes pattern-matching, LHASA evaluates each transform by reading and answering a list of scope-and-limitations questions, or qualifiers, which delineate precisely the molecular features required or prohibited by the transform. Knowledge base entries, including these qualifiers, are written in a special chemical English language, called CHMTRN, designed for LHASA and interpreted on-line by the program. Transforms passing all stages of this detailed evaluation are shown to the chemist, while failing transforms are killed and not shown. Strategy and Tactic Selection When planning a laboratory synthesis, the expert organic chemist does not simply apply every reaction that might be used to make the target structure and all intermediate structures. Rather, s/he identifies one or more strategies and tactics to guide the analysis in the direction of maximal retrosynthetic simplification of the target. In a similar fashion, LHASA uses strategies and tactics to emulate the chemists' reasoning and limit the scope of the search for transforms. There are five major strategies in LHASA: functional-group and pattern-based, topological or "strategic bond", key-transform, stereochemical, and starting-material-oriented. To assist the chemist in selecting strategies, a "LHASA Suggestions" mode has recently been implemented in which the program suggests tactics based on its perception of synthetically-significant structural features. Transform Knowledge Base The major focus of LHASA research at Harvard is in developing sophisticated algorithms for selecting and evaluating strategies, tactics, and transforms, rather than the writing of the transforms for the LHASA knowledge base. LHASA transforms are written to be very general, so that they can be applied to any target structure containing the correct retron, or keying substructure (ring, functional group arrangement, etc.). As such, they are difficult to write, since a multitude of structural possibilities must be considered, and also the necessary skills needed to write good CHMTRN take time to acquire. The LHASA knowledge base consists, at present, of some 2400 transforms and tactical combinations of transforms. A group of chemical and pharmaceutical companies in the United Kingdom has already dedicated considerable effort to knowledge- base expansion, with concentration in the area of heteroaromatic chemistry. A total of approximately 700 transforms in the LHASA knowledge base originate in the UK. Expansion of the knowledge base is continuing and recently an effort to update some of the older transforms has been undertaken. Other Related Software A small number of related programs have spun off from LHASA as well. While certain of these programs are of a proprietary nature, others are available for general use, among them DEREK (a substructure-based toxicology prediction program), APSO (a program for teaching principles of synthesis to organic chemistry students), and PROTECT (a graphically-oriented program for identification of protective groups in organic syntheses). Recently an interface to DEREK has been added to the LHASA program, allowing the chemist to directly use DEREK to process a precursor generated by LHASA and hence view the compounds predicted toxicology. International Distribution LHASA is used in approximately 20 industrial concerns and academic institutions world-wide. The LHASA group at Harvard maintains an ongoing collaboration with groups in several other universities, among them Leeds University (UK), the University of Helsinki, the University of Nijmegen (the Netherlands), and Chalmers Institute of Technology (Goteborg, Sweden). A non-profit corporation in the UK (LHASA UK, Ltd.) has also been formed to coordinate the expansion of knowledge bases for both LHASA and DEREK. Recent Literature Reviews E.J. Corey, A.K. Long, S.D. Rubenstein, Science 228 408 (1985). A.K. Long, S.D. Rubenstein, L.J. Joncas, Chemical and Engineering News, 22 (1983). For more information, contact: Dr. Alan K. Long Harvard Chemistry Dept. 12 Oxford Street Cambridge, MA 02138 UNITED STATES +1 617 495 4283 long : at : chemistry.harvard.edu ******************************************************************************** >From LHASA UK (jan "-at-" mi.leeds.ac.uk) Tue Dec 12 2:37:16 1994 Dear Sir, Just to let you know that there is an organisation called LHASA UK that distributes LHASA and CAMEO synthesis planning software to industrialists and academics in the UK and Europe. I will send (by post) information leaflets on this software to you. If you need to know any more, please get in touch. Yours sincerely, Dr. Jan J. Langowski LHASA UK Technical Manager -- ----------------------------------------------------------------------------- Robert K. Szilagyi University of Veszprem METMOD FF research fellow Dept. Org. Chem. L1 Email: szilagyi %-% at %-% miat0.vein.hu Veszprem, H-8201 L2 | R1 szilagyi (- at -) indy.mars.vein.hu Egyetem u. 10 >W=C< Phone: +36-(88)-422022/156 P.O.Box 158 L3 | R2 FAX: +36-(88)-426016 HUNGARY L4 http://indy.mars.vein.hu:8000/molmod.html -----------------------------------------------------------------------------