From jfm@mi.leeds.ac.uk Wed Jul 16 06:07:26 1997 Received: from gps1.leeds.ac.uk for jfm@mi.leeds.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA06247; Wed, 16 Jul 1997 05:09:57 -0400 (EDT) Received: from mi.leeds.ac.uk (misun1.leeds.ac.uk [129.11.12.4]) by gps1.leeds.ac.uk (8.8.5/8.8.5) with SMTP id KAA22616; Wed, 16 Jul 1997 10:09:54 +0100 (BST) Sender: jfm@mi.leeds.ac.uk Message-Id: <33CC8FE1.1CFB@mi.leeds.ac.uk> Date: Wed, 16 Jul 1997 10:09:53 +0100 From: Jean-Francois Marchaland X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) Mime-Version: 1.0 To: "Douglas A. Smith Ph.D." Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Re: CCL:Reaction Pathway Program References: <3.0.1.32.19970714221226.009b8fc0@pop.dasgroup.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Douglas, > > 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. Pure and Appl. Chem. vol.62, 10, pp 1921 "Abstract- An interactive computer program, CAMEO, has been developed to predict products of organic reactions given the starting materials and conditions...." At the beginning CAMEO was a reaction simulator, but is there a new module now in CAMEO that " 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. > I don't know if they are all maintained and commercialized but a lots of Computer Assisted Organic Synthesis (CAOS) programs that works in a retrosynthetic way have been designed. I suggest you to have a look at: "Computer-assisted Solution of Chemical Problems - The historical Development and the Present State of the Art of a New discipline of Chemistry" by Ivar Ugi and al. in Angew. Chem. Int. Ed. Engl. 1993, 32, 201-227 It's a huge review on computer chemistry, but a good part of it deals with CAOS. Now if you want a quick answer on one of the commercial products, try http://www.chem.leeds.ac.uk/LUK/ Hope it helps Jean-Francois Marchaland _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Dr J.F. Marchaland jfm@mi.leeds.ac.uk _/ _/ ICAMS, School of Chemistry UK: 0113 233 6567 _/ _/ University of Leeds internat.: +44 113 233 6567 _/ _/ LS29JT LEEDS FAX: 6563 _/ _/ _/ _/ http://chem.leeds.ac.uk/ICAMS/people/jfm.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From ccl@www.ccl.net Wed Jul 16 08:07:31 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id HAA06694; Wed, 16 Jul 1997 07:42:38 -0400 (EDT) Received: from nazgul.mpiz-koeln.mpg.de for abdallah@mpiz-koeln.mpg.de by bedrock.ccl.net (8.8.6/950822.1) id HAA21888; Wed, 16 Jul 1997 07:42:34 -0400 (EDT) Received: (qmail 20022 invoked from network); 16 Jul 1997 11:45:21 -0000 Received: from nazgul.mpiz-koeln.mpg.de (@193.174.239.40) by nazgul.mpiz-koeln.mpg.de with SMTP; 16 Jul 1997 11:45:21 -0000 Date: Wed, 16 Jul 1997 13:45:21 +0200 (MDT) From: Fuad Abdallah Reply-To: Fuad Abdallah To: chemistry@ccl.net Subject: Re: What languages will be here tomorrow... In-Reply-To: <199707132338.AA23677@world.std.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Members, it is very interesting to note, that the discussion about the programming languages for scientific programs only mentioned Fortran, C, C++ and Python. Although i do understand that everybody tries to use as much existing code as possible i do also see many disadvantages. From the point of Software Engineering it will become more and more difficult to improve (or even maintain) the huge scientific software projects. Even if C++ tries to overcome some of the problems of software reusability, it introduces some new problems that already have been mentioned in earlier mails to the CCL. I do not agree that it is always important to use the language that produces the fastest executables. Even if the choice of Fortran (or whatever you consider to be "the fastest" programming language) would give your executables a constant factor of execution speed advantage it could take a _very_ long time to implement new, improved algorithms. The concepts underlying Fortran, C and C++ is in deed very old. Although many of these "imperative language" have been developed over the last years and there is a steady addition of new features, resulting in more and more complex languages, the fundamental concept based on the computer model designed by von Neumann, did not change. Taking all this together, i do see a strong need for new concepts and i think a promising new approach are the functional programming languages like ML, Haskell, Gofer and Clean. They offer many interesting features like higher order functions, polymorphism and straight forward parallelism (a _very_ important point if you consider the fact that more and more multiprocessor systems are being used) and allow programming on a much higher level of abstraction, enabling the programmer the fast implementation of new algorithms. If you are interested in FP, have a look at the FAQ: http://www.cs.nott.ac.uk/Department/Staff/gmh/faq.html best regards, Fuad -- Fuad Abdallah Max-Planck-Institut fuer Zuechtungsforschung / ZWDV From mclark@smtpgwy.isinet.com Wed Jul 16 09:22:29 1997 Received: from isinet.com for mclark@smtpgwy.isinet.com by www.ccl.net (8.8.3/950822.1) id IAA06882; Wed, 16 Jul 1997 08:19:17 -0400 (EDT) From: Received: from smtpgwy.isinet.com ([198.62.99.211]) by pandora.isinet.com with SMTP id <18443>; Wed, 16 Jul 1997 08:21:01 -0400 Received: from ccMail by smtpgwy.isinet.com (SMTPLINK V2.11.01) id AA869066495; Wed, 16 Jul 97 08:16:29 EST Date: Wed, 16 Jul 1997 09:16:29 -0400 Message-Id: <9706168690.AA869066495@smtpgwy.isinet.com> To: wjs@csb0.ipc.pku.edu.cn, wdi@eros.ccc.uni-erlangen.de Cc: chemistry@www.ccl.net Subject: Re: CCL:Re: CCL:Where is software on interconversion of chem There are some software packages for Wiswesser notation. You can contact Fraser-Williams for either the software, or they can convert from the WLN database for you on a consulting basis. ______________________________ Reply Separator _________________________________ Subject: CCL:Re: CCL:Where is software on interconversion of chemical Author: wdi@eros.ccc.uni-erlangen.de at INTERNET Date: 7/15/97 7:56 PM On Jul 14, 16:52, Wang Jiansuo wrote: > Subject: CCL:Where is software on interconversion of chemical structure sy > Dear netter, > Wiswesser Line Notation(WLN) is a widely-used method of chemical I HOPE NOT! This kind of notation is an abomination. Are there any software packages around which stil use this represenation? This format was designed at a time when storage space was extremely expensive. It produces very compact representations, at the cost of ridiculously convoluted and self-contradicting encoding rules. If you need to use a line notation, you should employ the widely supported SMILES system. If, however, you have some legacy database, you have my deepest sympathy and a lot of work to do. > structure presentation.I am looking for programs that interconve between > WLN and Connection Table or other structure presentation systems.Any > information of yours is appreciated. > Thanks in advance. > Your sincerely, > >-- End of excerpt from Wang Jiansuo -- 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 --- 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 --- From jerickson@dowelanco.com Wed Jul 16 13:10:23 1997 Received: from elinet1.dowelanco.com for jerickson@dowelanco.com by www.ccl.net (8.8.3/950822.1) id MAA08194; Wed, 16 Jul 1997 12:49:52 -0400 (EDT) Received: by elinet1.dowelanco.com id AA25789 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Wed, 16 Jul 1997 11:49:48 -0500 Received: by elinet1.dowelanco.com (Internal Mail Agent-1); Wed, 16 Jul 1997 11:49:48 -0500 Message-Id: From: "Erickson, Jon" To: "'Gina Barbeau'" Cc: "'chemistry@www.ccl.net'" Subject: RE: A request for help on molecular modeling simulations. Date: Wed, 16 Jul 1997 11:50:58 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Gina, There is an excellent paper by Ajay and Mark Murcko that discusses computational binding energies that may answer some of your general questions. See: J. Med. Chem., 1995, 38, 4953. Jon Erickson DowElanco CAMD >---------- >From: Gina Barbeau[SMTP:gbarbeau@eagle.ibc.edu] >Sent: Wednesday, July 16, 1997 10:43 AM >To: chemistry@www.ccl.net >Subject: CCL:A request for help on molecular modeling simulations. > >I am an undergrad Biochem student doing summer research on ligand-receptor >interactions. I would like to know what are good energy values to expect >when docking the protein ligand to the protein receptor. What kind of >values should I be looking for in the VDW, the electrical energy, and the >overall energy? How do I estimate that the energy is a good docking of >the two? >The software that I have to work with is Insight II on the SGI. > >I would also appreciate any suggestions as to what minimization and >dynamics algorithms to use on Discover once I dock the two together to get >a better idea of "docked" conformation. > >In advance, thank you for your help. >G. Barbeau >email: gbarbeau@eagle.ibc.edu > > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: gbarbeau@eagle.ibc.edu >-- Original Sender From: Address: gbarbeau@eagle.ibc.edu >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 > >