From MAILER-DAEMON@www.ccl.net Thu Jul 17 12:20:57 1997 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA14309; Thu, 17 Jul 1997 12:02:32 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id SAA03974; Thu, 17 Jul 1997 18:02:52 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9707171802.ZM3972@eros.ccc.uni-erlangen.de> Date: Thu, 17 Jul 1997 18:02:42 -0600 In-Reply-To: kcross@cas.org (Kevin P. Cross Ext. 3192) "CCL:SUMMARY - Reaction Pathway Programs" (Jul 17, 10:53) References: <9707171053.AA29958@cas.org> Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: kcross@cas.org (Kevin P. Cross Ext. 3192) Subject: Re: CCL:SUMMARY - Reaction Pathway Programs Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jul 17, 10:53, Kevin P. Cross Ext. 3192 wrote: > Subject: CCL:SUMMARY - Reaction Pathway Programs > Folks, > > Joe has done a nice job gathering and summarizing > information about retro-synthesis planning programs. > I would like to have this conversion move in a slightly > different direction. A lot of these programs have been > around for a long time yet it seems that none has really > caught on in the market place. > > What are peoples opinions on why these programs are not > routinely used for synthesis planning today? > > I have a few questions to start out: > > Do they give too many hypothetical answers but not practical? > Do they give too many answers (or repetative answers - same substructure)? > Is the software too difficult to use without a lot of training? > Does the software fail to reveal anything new to trained synthetic chemists? > Is it too expensive or run on the wrong platforms? > Does it lack integration with reaction data, availability, etc? > Is it too time consuming to run for many users? > > What can be done to make these programs more useful? > > Many thanks in advance, > Kevin See Angew. Chemie Int. Ed. 34, 1995, 2613-2633 -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From tune@qcl.t.u-tokyo.ac.jp Thu Jul 17 23:07:49 1997 Received: from deneb.qcl.t.u-tokyo.ac.jp for tune@qcl.t.u-tokyo.ac.jp by www.ccl.net (8.8.3/950822.1) id WAA17888; Thu, 17 Jul 1997 22:16:29 -0400 (EDT) Received: (from tune@localhost) by deneb.qcl.t.u-tokyo.ac.jp (8.8.5/3.4W4-961025) id LAA60537; Fri, 18 Jul 1997 11:15:18 +0900 Date: Fri, 18 Jul 1997 11:15:18 +0900 Message-Id: <199707180215.LAA60537@deneb.qcl.t.u-tokyo.ac.jp> To: take@qcl.t.u-tokyo.ac.jp Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:SUMMARY - Reaction Pathway Programs In-Reply-To: Your message of Tue, 15 Jul 1997 16:51:21 -0500. <199707152152.AA20799@interlock.amoco.com> From: tune@qcl.t.u-tokyo.ac.jp (Takao Tsuneda) X-Mailer: mnews [version 1.19PL2] 1996-01/26(Fri) 関係なかったら捨てて下さい。 > Hi CCL: > > Below is the summary of responses to the "retro-synthesis" question > I recently asked. Thanks to all who have responded. I have edited > some of the answers and so I take full responsibility for any errors. > If I get any more answers, I will re-post summary. > > << Tue Jul 15 16:50:53 CDT 1997 >> > > > Execute Summary of Answers > > 1) SYNGEN, Jim Hendrickson, Brandeis University > 2) CAMEO, Bill Jorgensen, Yale > 3) SYNTREE, Commerical Software, Vendor? > 4) SYNLIB, Dan Chodosh, may not exist anymore > 5) REACCS, MDL > 6) CAS's reaction data base > 7) Chiron, Steve Hannisan (spl?) of U. of Montreal. > 8) LAHSA, E.J. Corey, Harvard U. > 9) Unknow, Michael Mavrovouniotis, Northwestern > 10) Crossfile, Beilstein > > :Joe > jtgolab@amoco.com > (630) 961-7878 > > ______________________________ Original Note __________________________________ > Subject: CCL:Reaction Pathway Program > Author: chemistry-request (chemistry-request@www.ccl.net) at unix,sh > Date: 7/14/97 4:43 PM > > Dear CCL Member: > > Do you know of any (engineering, chemistry, biological, etc) program that > given a compound would suggest any and all reaction pathways toward that > compound (no matter how outlandish from a thermodyanmic standpoint)? > > For example, given tolune, the program would suggest: > > 1) benzene + methane -> toluene > 2) methylcyclohexane -> toluene + H2 > 3) methane + heat/pressure -> toluene + H2 > 4) ETC. > > Perhaps this is really a database that is part of a program. Any leads > would be gratefully appreciated! Thanks. > > _____________________________Reply Separator_________________________________ > Subject: Re: CCL:Reaction Pathway Program > Author: lchen (lchen@mdli.com) at unix,mime > Date: 7/14/97 5:16 PM > > Dear Joe: > > Please check the following SYNGEN site: > > http://syngen2.chem.brandeis.edu/syngen.html > > you may find something interesting you. > > -Lingran > > ********************************************************** > Lingran Chen, Ph.D. > Senior Scientific Programmer > MDL Information Systems, Inc. > 14600 Catalina Street > San Leandro > CA 94577 > > Phone: (510) 895-1313, Ext. 1305 > FAX: (510) 614-3616 > > Email: LCHEN@MDLI.COM > URL: http://www.mdli.com > http://syngen2.chem.brandeis.edu/~chen/lingran.html > ********************************************************** > > _____________________________Reply Separator_________________________________ > Subject: Re: CCL:Reaction Pathway Program > Author: eslone (eslone@patriot.net) at unix,mime > Date: 7/14/97 6:32 PM > > Talk to Jim Hendrickson at Brandeis University. He has a program called > SynGen. > ___________________________________________________________________ > > J. Eric Slone > Scientific Consulting Services > 5500 Holmes Run Parkway, Suite 501 > Alexandria, Virginia 22304-2851 > > Phone: (703) 461-7078 mailto:eslone@patriot.net > Fax: (703) 751-6639 http://www.patriot.net/users/eslone > ___________________________________________________________________ > > _____________________________Reply Separator_________________________________ > Subject: Re: CCL:Reaction Pathway Program > Author: dsmith (dsmith@CTCnet.Net) at unix,mime > Date: 7/14/97 9:12 PM > > Joe: > > I am not familiar with any program that will suggest ALL reaction > pathways... there are just way too many possibilities, which is why we > still have synthetic organic chemists. > > You are probably familiar with Bill Jorgensen's CAMEO program (I hope I > have the name correct), which can suggest 'reasonable' synthetic routes to > various types of compounds and functionality. There is also a commercial > program (not that Bill doesn't sell his programs, ;)) called SYNTREE (I > believe). There were some papers about this at either the last ACS > National meeting in San Francisco or at the Midland, MI, ACS Regional > meeting in May. I can look for more information if you wish, but I am at > home and just finishing up a vacation while I write this. > > Regardless, both of these programs use a combination (I believe) of data > bases and "expert" algorithms to select likely reactions. I don't know of > anything that will give you all possible routes, except perhaps an > aggressive undergraduate who has just finished his/her organic final exam. > > There was also SYNLIB that came from the late Dan Chodosh... I don't know > if anyone picked up that program so I can't tell you if it still exists. > This was purely data base based and matched based on user-defined > descriptors, if I remember correctly from my postdoc days. MDL REACCS and > CAS's reaction data base are two others that come to mind. > > I would also love to hear from anyone else about similar programs. Please > post to CCL rather than just to Joe. > > Doug Smith > > -- > Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 > The DASGroup, Inc. | fax: (814) 255-3517 > 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com > Johnstown, PA 15905 | WWW: http://www.dasgroup.com > > Contract R&D specialists in modeling, simulation, synthesis and risk > assessment for chemistry, materials science, and biotechnology. > > _____________________________Reply Separator_________________________________ > Subject: Re: CCL:Reaction Pathway Program > Author: Willie (Willie@microsimulations.com) at unix,mime > Date: 7/15/97 1:12 AM > > Joe, > > Two programs that can do retrosynthetic analysis, > 1. Chiron, from Prof. Steve Hannisan (wrong spelling?) of U. of Montreal. > 2. LAHSA, from prof. E.J. Corey of Harvard U. > > -- > Willie Cui, Ph.D. voice 201-512-0486 > MicroSimulations fax: 201-512-0489 > 478 Green Mountain Rd. email: willie@microsimulations.com > Mahwah, NJ 07430 URL: http://www.microsimulations.com > > _____________________________Reply Separator_________________________________ > Subject: RE: Reaction Pathway Program > Author: RICHEYFA (RICHEYFA@ucarb.com) at unix,mime > Date: 7/15/97 6:12 AM > > Hi, Joe, > > I had a similar question when looking for new routes to commodity > chemicals. I found references to techniques for making expensive > [usually pharmaceutical] chemicals which would take a target structure > and elaborate[!] multistep pathways from known precursors. I think one > was E.J. Corey's group's product. At least one of these gave > synthetically viable guesses for transformations so probably weeded out > a lot of the thermodynamically infeasible routes. > > I haven't pursued this very far but was left with the feeling that there > was a lot of work in the 80's and the only thing that has survived > outside academe has been the pharmaceutical part. I may be wrong in > this. > > I never did summarize my work but if you are interested I can send you > references with brief comments. > > I wanted this approach to automate the cataloging of possible synthetic > routes including finding the ones that I'd overlook because of my > particular chemical background. > > Forrest Richey > > Union Carbide Corporation > Technical Center > Bldg 740 Room 4107 > S. Charleston, WV 25303 > (304)747-4964 > > Two things happen when you reach fifty, and if I could remember one, I > wouldn't worry about the other two. > > _____________________________Reply Separator_________________________________ > Subject: Reaction Pathways > Author: burkhart (burkhart@goodyear.com) at unix,mime > Date: 7/15/97 9:00 AM > > Hi Joe, > > If I'm not mistaken, Prof. Bill Jorgensen's group @Yale worked > on a program called CAMEO. As I remember it, they were trying > to use it as a reaction chemistry "assistant"--but I'm not > sure how far they got. > > ----------------------------------+------------------------------------ > Papernet: Craig W. Burkhart | Baseball & summer--What could be > Goodyear Research | better? The birds are singing and > 142 Goodyear Blvd. | the BATS are out! > Akron, OH 44305 | Indians update: 48-37 (.564) > Mouthnet: 330.796.3163 | 'Best little .500 club' $60 mil > Faxnet: .3304 | can buy... (swampland, anyone?) > Internet: cburkhart@goodyear.com | Pitching REALLY Stinks!!! UGH! > ----------------------------------+------------------------------------ > > _____________________________Reply Separator_________________________________ > Subject: Re: CCL-Reaction Pathway Pro > Author: mnliebman (mnliebman@vysis.com) at unix,sh > Date: 7/15/97 9:59 AM > > RE>CCL:Reaction Pathway Program 7/15/97 > > Joe > try contactine Michael Mavrovouniotis at Northwestern- mlmavro@nwu.edu I > think > Michael > 271 7190 > _____________________________Reply Separator_________________________________ > Subject: Your e-mail to CCL > Author: pierre (pierre@mdli.com) at unix,mime > Date: 7/15/97 10:14 AM > > Dear Joe, > > I received a copy of your e-mail attached at the end of my reply. You may > remember that we talked on the phone a few month ago. Although my answer is > obviously biased by the fact that I work for MDL, my experience after 9 > years working with the large pharma and chemical industries in Europe and in > the US is that there seems to be no good way to have a prediction program. A > lot of companies have tried, and they have ended up licensing our databases > or other (like Beilstein Crossfire). The advantage they have found in our > system, compared to other database systems, (especially since we introduced > ISIS, the client server system we provide now) is the flexibility of our > querying interface. You can search not only on exact reactions, but also on > things like " find an example of a reaction where this fragment is formed". > Or "find an example of a reaction using these conditions where a fragment is > unaltered". > > As an example, to address your query below, we would draw the toluene, and > define it as a product, and then we would perform a search known as > "structure as product not as reactant, or "sub-structure as product, not as > reactant". Which basically defines that the toluene has to be formed during > the reaction. You could also refine the query by specifying certain classes > of reactions you do not want (list catalysts that are expensive etc). > > Running the query you use as an example on our databases leaded to 113 > reactions out of 107 publications. The query was exclusively dealing with > the toluene as product, no substituted toluene was allowed. In some of these > reactions the benzene is a by product, and probably a lot of them are > dealing with cleavage from a larger structure, but these reactions could > still be of interest, you would have to judge. > > >> [Parts of Original Message Edited/Deleted] << > > Sincerely > > Pierre Allemand Ph.D. > Senior Account Manager > > >-- END > > -- > > :Joe > jtgolab@amoco.com > (630) 961-7878 > > +---------------------------------------------------------+ > | You can pick your friends but you can't pick your nose. | > +---------------------------------------------------------+ > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > では。 -------------------------------- T. Tsuneda Graduate School of Engineering The University of Tokyo Tokyo 113, Japan