From chemistry-request@server.ccl.net Thu Jun 1 02:37:44 2000 Received: from dns.campus.mlsultan.ac.za ([196.13.103.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA19133 for ; Thu, 1 Jun 2000 02:37:35 -0400 Received: from wpogate.mlsultan.ac.za (wpogate.campus.mlsultan.ac.za [196.13.102.11]) by dns.campus.mlsultan.ac.za (AIX4.2/UCB 8.7/8.7) with SMTP id IAA11092 for ; Thu, 1 Jun 2000 08:55:34 +0300 (USADT) Received: from MLSTGW-Message_Server by wpogate.mlsultan.ac.za with Novell_GroupWise; Thu, 01 Jun 2000 08:34:30 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5.3 Date: Thu, 01 Jun 2000 08:33:58 +0200 From: "Thishana Singh" To: , " Subject: Frequency Calculation Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id CAA19135 Dear all I have been trying to run a FREQ job on a cage lactam. The job with the following input was done on PC and completed with no problems. _______________________________________________________ %chk=m1s10q #N ONIOM(RHF/STO-3G:PM3) GEOM=CHECKPOINT FREQ Mech1str10 - product - FREQ 1 1 ________________________________________________________ However, when the input is changed to 6-31G** the job crashes giving a "CONVERGENCE FAILURE" error message. The higher level job is run on a DEC Alpha. I appreciate some advice since I am new in the field. Thank you. Thishana Singh M L Sultan Technikon Department of Chemistry 41/43 Centennary Road Durban 4000 South Africa Telephone : 27 31 3085521/2/3 Fax : 27 31 3085400 email : singht@wpo.mlsultan.ac.za From chemistry-request@server.ccl.net Thu Jun 1 02:37:49 2000 Received: from dns.campus.mlsultan.ac.za ([196.13.103.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA19134 for ; Thu, 1 Jun 2000 02:37:39 -0400 Received: from wpogate.mlsultan.ac.za (wpogate.campus.mlsultan.ac.za [196.13.102.11]) by dns.campus.mlsultan.ac.za (AIX4.2/UCB 8.7/8.7) with SMTP id IAA17240 for ; Thu, 1 Jun 2000 08:55:34 +0300 (USADT) Received: from MLSTGW-Message_Server by wpogate.mlsultan.ac.za with Novell_GroupWise; Thu, 01 Jun 2000 08:34:30 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5.3 Date: Thu, 01 Jun 2000 08:33:58 +0200 From: "Thishana Singh" To: , " Subject: Frequency Calculation Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id CAA19139 Dear all I have been trying to run a FREQ job on a cage lactam. The job with the following input was done on PC and completed with no problems. _______________________________________________________ %chk=m1s10q #N ONIOM(RHF/STO-3G:PM3) GEOM=CHECKPOINT FREQ Mech1str10 - product - FREQ 1 1 ________________________________________________________ However, when the input is changed to 6-31G** the job crashes giving a "CONVERGENCE FAILURE" error message. The higher level job is run on a DEC Alpha. I appreciate some advice since I am new in the field. Thank you. Thishana Singh M L Sultan Technikon Department of Chemistry 41/43 Centennary Road Durban 4000 South Africa Telephone : 27 31 3085521/2/3 Fax : 27 31 3085400 email : singht@wpo.mlsultan.ac.za From chemistry-request@server.ccl.net Thu Jun 1 05:08:46 2000 Received: from buckholdtassociates.com (async52-6.nas.onetel.net.uk [212.67.102.52]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA20078 for ; Thu, 1 Jun 2000 05:08:45 -0400 Date: Thu, 1 Jun 2000 05:08:45 -0400 From: links@buckholdtassociates.com Message-Id: <200006010908.FAA20078@server.ccl.net> Reply-To: links@buckholdtassociates.com To: CHEMISTRY@ccl.net Subject: Request for link Hello I came across your site today and was interested in the like minded nature of its content with my own. In fact the Self Esteem Advisory Service set up around 3 years ago now attracts visitors from all over the world. I have found that they are interested in not only my site but also the content of other sites that expand or complement our own material. I was wondering if you would like a link from our website to yours. It is all automated and you can just add yourself. I would appreciate a link in return. I look forward to hearing from you - many thanks Elizabeth Elizabeth Morris BA(psych). MAHPP Buckholdt Associates www.buckholdtassociates.com/seas.htm From chemistry-request@server.ccl.net Wed May 31 06:45:25 2000 Received: from samolus.sdi.slu.se (samolus.sdi.slu.se [130.238.100.201]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA13583; Wed, 31 May 2000 06:45:24 -0400 Received: from sdi.slu.se (localhost [127.0.0.1]) by samolus.sdi.slu.se (8.8.8/8.6.6) with ESMTP id MAA08213; Wed, 31 May 2000 12:45:12 +0200 (MET DST) Sender: hanslil@samolus.sdi.slu.se Message-ID: <3934ED37.F753D261@sdi.slu.se> Date: Wed, 31 May 2000 12:45:12 +0200 From: Hans =?iso-8859-1?Q?Liljenstr=F6m?= Organization: SLU and Agora for Biosystems X-Mailer: Mozilla 4.73 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: chemistry-request@ccl.net, jkl@ccl.net, chemistry@ccl.net Subject: Conference announcement Content-Type: multipart/alternative; boundary="------------8314590225DCB0CF31E8597F" --------------8314590225DCB0CF31E8597F Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Sirs, I just recently learnt about your website and lists, and wonder if you could announce the following meeting on your site/lists, since I believe the meeting also overlaps with your interest groups. Thank you. Yours sincerely, Hans Liljenström, director Agora for Biosystem NORDIC SYMPOSIUM ON COMPUTATIONAL BIOLOGY 2000 18-23 JUNE 2000 AGORA FOR BIOSYSTEMS, SIGTUNA, SWEDEN Co-organized by Agora for Biosystems and Nordita An updated version of the program is available on http://www.agora.kva.se/meetings/CompBio2000/program.html The symposium addresses questions of high current interest in biology and related.fields. The main focus is on bioinformatics, but computational methods applied to molecular and cellular biology, as well as computational neurobiology and ecology will also be included. The symposium is primarily intended to attract young scientists in the Nordic and surrounding countries, but all interested are welcome as long as space allows. A major objective is to give an introduction to some of the most important problems and challenges within the field. This will be accomplished by several tutorials, in addition to invited talks given by top scientists from abroad and from the region. There will also be ample time for poster presentations and for formal and informal discussions. TOPICS INCLUDE: - Bioinformatics - Macromolecular dynamics - Computational (functional) genomics - Computational neurobiology - Computational ecology INVITED SPEAKERS INCLUDE: Edward Cox, Dept. of Molecular Biology, Princeton University Mats Gyllenberg, Dept. of Mathematics, University of Turku John Hopfield, Dept. of Molecular Biology, Princeton University Eric Jakobsson, Dept. of Molecular and Integrative Physiology, University of Illinois Inge Jonassen, Dept. of Informatics, University of Bergen Erik Lindahl, Dept. of Physics, Royal Institute of Technology Kristian Lindgren, Dept. of Physical Resource Theory, Chalmers and Göteborg University Michael Mackey, Department of Physiology, McGill University Johan Paulsson, Dept. of Molecular Biology, Uppsala University Hans Plesser, Dept. of Physics, Göttingen Dirk Repsilber, Inst. for Forest Genetics and Forest Tree Breeding, University of Hamburg Mattias Wahde, Dept. of Mechanical Engineering, Chalmers ORGANIZING COMMITTEE Soren Brunak, Center for Biological Sequence Analysis, Technical University of Denmark Olle Edholm, Theoretical Physics, Royal Institute of Technology, Stockholm Gaute Einevoll, Dept. of Physics, Agricultural University of Norway Jarl-Thure Eriksson, Electrical Engineering Labs, Tampere University Gunnar von Heijne, Center for Bioinformatics, Stockholm University John Hertz, Nordita, Copenhagen Hans Liljenström, Agora for Biosystems, Sigtuna Dietrich von Rosen, Dept. of Biometrics, SLU, Uppsala More information and registration form can be obtained: - http://www.agora.kva.se/meetings/CompBio2000 Please register electronically using a web browser if possible. Abstract submissions can also be made via the online registration form. - email: hans.liljenstrom@sdi.slu.se - by mail: Hans Liljenstrom Dept. of Biometrics, SLU Box 7013 SE-750 07 Uppsala Sweden FAX: +46-18-673502 --------------8314590225DCB0CF31E8597F Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Sirs,

I just recently learnt about your website and lists, and wonder if you could announce the following meeting on your site/lists, since I believe the meeting also overlaps with your interest groups. Thank you.

    Yours sincerely,

    Hans Liljenström, director
    Agora for Biosystem
 

NORDIC SYMPOSIUM ON COMPUTATIONAL BIOLOGY 2000

18-23 JUNE 2000

AGORA FOR BIOSYSTEMS, SIGTUNA, SWEDEN

Co-organized by Agora for Biosystems and Nordita

An updated version of the program is available on
http://www.agora.kva.se/meetings/CompBio2000/program.html

The symposium addresses questions of high current interest in biology and related.fields. The main focus is on bioinformatics, but computational methods applied to molecular and cellular biology, as well as computational neurobiology and ecology will also be included.

The symposium is primarily intended to attract young scientists in the Nordic and surrounding countries, but all interested are welcome as long as space allows. A major objective is to give an introduction to some of the most important problems and challenges within the field. This will be accomplished by several tutorials, in addition to invited talks given by top scientists from abroad and from the region. There will also be ample time for poster presentations and for formal and informal discussions.

TOPICS INCLUDE:
- Bioinformatics
- Macromolecular dynamics
- Computational (functional) genomics
- Computational neurobiology
- Computational ecology

INVITED SPEAKERS INCLUDE:
Edward Cox,  Dept. of Molecular Biology, Princeton University
Mats Gyllenberg, Dept. of Mathematics, University of Turku
John Hopfield, Dept. of Molecular Biology, Princeton University
Eric Jakobsson, Dept. of Molecular and Integrative Physiology, University of Illinois
Inge Jonassen, Dept. of Informatics, University of Bergen
Erik Lindahl, Dept. of Physics, Royal Institute of Technology
Kristian Lindgren, Dept. of Physical Resource Theory, Chalmers and Göteborg University
Michael Mackey, Department of Physiology, McGill University
Johan Paulsson, Dept. of Molecular Biology, Uppsala University
Hans Plesser, Dept. of Physics, Göttingen
Dirk Repsilber, Inst. for Forest Genetics and Forest Tree Breeding, University of Hamburg
Mattias Wahde, Dept. of Mechanical Engineering, Chalmers

ORGANIZING COMMITTEE
Soren Brunak, Center for Biological Sequence Analysis, Technical University of Denmark
Olle Edholm, Theoretical Physics, Royal Institute of Technology, Stockholm
Gaute Einevoll, Dept. of Physics, Agricultural University of Norway
Jarl-Thure Eriksson, Electrical Engineering Labs, Tampere University
Gunnar von Heijne, Center for Bioinformatics, Stockholm University
John Hertz, Nordita, Copenhagen
Hans Liljenström, Agora for Biosystems, Sigtuna
Dietrich von Rosen, Dept. of Biometrics, SLU, Uppsala

More information and registration form can be obtained:

   - http://www.agora.kva.se/meetings/CompBio2000
     Please register electronically using a web browser if possible.
    Abstract submissions can also be made via the online registration form.

   - email: hans.liljenstrom@sdi.slu.se
   - by mail:  Hans Liljenstrom
                      Dept. of Biometrics, SLU
                      Box 7013
                      SE-750 07 Uppsala
                      Sweden
                      FAX: +46-18-673502 --------------8314590225DCB0CF31E8597F-- From chemistry-request@server.ccl.net Wed May 31 09:44:53 2000 Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA15249 for ; Wed, 31 May 2000 09:44:53 -0400 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id OAA27726; Wed, 31 May 2000 14:44:14 +0100 (BST) Message-ID: <39351873.C932AA3D@nibsc.ac.uk> Date: Wed, 31 May 2000 14:49:39 +0100 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: Galina Chaban CC: chemistry@ccl.net Subject: Re: CCL:OPLS-AA in Tinker References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Galina As I understand it the procedure with adding parameters to Tinker is the following 1) Make sure that every atom in the tinker coordinate (.xyz) file has an atom type defined - eg 21 for the carboxylic C atom in your example. 2) Look in the relevant .key file to find the name of the parameter file (.prm) that is being used. 3) make an entry in the .prm file of the format bond 21 26 656.0 1.250 ^ ^ force bond constant length 4) One you fix up the bond length parameters, you will most likely have to do the same for angle and torsion types. 5) To test the parameter file modifications run the analyze.x program using your .xyz and .key files as input. Hope this helps. Mark F Galina Chaban wrote: > Hello everyone, > > I would like to do a calculation of glycine molecule using > Tinker program and OPLS-AA potential. > > I wanted to use these atom types for glycine carboxyl group: > atom 107 21 C "COOH Carboxylic Acid" 6 12.000 3 > atom 108 26 OH "OH Carboxylic Acid" 8 15.999 2 > atom 109 22 O "C=O Carboxylic Acid" 8 15.999 1 > atom 110 8 HO "COOH Carboxylic Acid" 1 1.008 1 > and these for amine group: > atom 70 19 NT "NH2 Primary Amine" 7 14.007 3 > atom 71 20 H2 "HN Primary Amine" 1 1.008 1 > > However, when I try to run it, the program stops with the message that > some parameters are not found. When I check the parameters file, > I can see that indeed many parameters are missing: for example, > bond parameters for atom pairs 21-26, 26-8, 19-20. > > Has anyone experienced this problem? How could I get the missing > parameter values? > I would appreciate any suggestions and references that could help. > > Galina > ------------------------------------------------------------------- > Dr. Galina Chaban > Fritz Haber Research Center for > Molecular Dynamics. > Hebrew University of Jerusalem > Jerusalem, Israel 91904 > Tel: 972-2-6585936 > Fax: 972-2-6513742 > e-mail: galinac@fh.huji.ac.il > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Thu Jun 1 09:22:54 2000 Received: from mail1.mclink.it (net128-007.mclink.it [195.110.128.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA22142 for ; Thu, 1 Jun 2000 09:22:48 -0400 Received: from Attila (net138-155.mclink.it [195.110.138.155]) by mail1.mclink.it (8.9.1/8.9.0) with SMTP id PAA27448; Thu, 1 Jun 2000 15:22:18 +0200 (CEST) Message-ID: <006001bfcbcc$d769b820$070000c0@CADD> From: "Elena Fioravanzo" To: "ccl" Cc: , , , Subject: Summary: Molecular Diversity - 2 Date: Thu, 1 Jun 2000 14:54:35 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear CCL members, Please find my original question and replies (new and old ones). Thanks a lot to collegues who contributed. ================= there are many methods and indices to estimate molecular similarity, but it is quite difficult to estimate-calculate molecular diversity. Could someone give me, please, references (articles, web-site, softwares) about this point? ================= A >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> These are other articles you might find useful: 1) "Measuring Molecular Diversity: Evaluation of Alternative Subsets Selected from Reagent Building Block Libraries for Combinatorial Chemistry." Blankley, C. J., Pharm. Pharmacol. Commun. 1998, 4, pages 139-146 2) "The Diversity Challenge in Combinatorial Chemistry." Kauvar, L. M. and Laborde, E., Drug Discovery and Development 1998, 1, pages 66-70 3) "Validated Descriptors for Diversity Measurements and Optimization." Martin, Y. C., Bures, M. G. and Brown, R. D., Pharm. Pharmacol. Commun. 1998, 4, pages 147-152 4) "Assesing Similarity and Diversity of Combinatorial Libraries by Spatial Autocorrelation Functions and Neural Networks." Sadowski, J., Wagener, M. and Gasteiger, J., Angew. Chem. Int. Ed. Engl. 1995, 34, pages 2674-2677 5) "Novel Software Tools for Addressing Chemical Diversity" R. S. Pearlman, Laboratory for Molecular Graphics and Theoretical Modeling, College of Pharmacy, University of Texas (From June/July, 1996). You can read this article on line at http://www.netsci.org/Science/Combichem/feature08.html 6) "Computational methods in molecular diversity and combinatorial chemistry." Bures, M.G., and Martin, Y.C., Curr. Opin. Chem. Biol. 1998, 2, pages 376-380 7) "Targeted molecular diversity in drug discovery: Integration of structure-based design and combinatorial chemistry." Li, J., Murray, C.W., Waszkowycz, B., and Young, S.C., Drug Discovery Today 1998, 3, pages 105-112 I hope this helps. Guillermo Morales ----- Guillermo A. Morales Morales Consulting E-mail: morales@combichemlab.com Website: http://www.combichemlab.com Member of the Combi-Web Consortium: http://www.combi-web.com B >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Elena, We have written three very extensive reviews on the subject. Note that the last one is still in press. Hope that helps. 1. D. K. Agrafiotis*, "Diversity of chemical libraries", in The Encyclopedia of Computational Chemistry; Schleyer, P.v.R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer III, H. F.; Schreiner, P. R., Eds., John Wiley and Sons, Chichester, 1998, Vol. 1, 742-761. 2. D. K. Agrafiotis*, J. P. Myslik, and F. R. Salemme, "Advances in diversity profiling and combinatorial series design", in Annual Reports in Combinatorial Chemistry and Molecular Diversity, Pavia, M., and Moos, W., Eds., Kluwer, 1999, 2, 71-92. 3. D. K. Agrafiotis*, V. S. Lobanov, D. N. Rassokhin, and S. Izrailev, "The measurement of molecular diversity", in Virtual Screening of Bioactive Molecules, H.-J. Böhm, H.-J., and Schneider, G., Eds., Wiley-VCH, Weinheim, in press. --- Dimitris K. Agrafiotis, PhD | E-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | Tel: (610) 458-6045 665 Stockton Drive, Suite 104 | Fax: (610) 458-8249 Exton, PA 19341 C >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Elena, I wrote a little program which helps you to select a maximally diverse subset of compounds from a large set of compounds, based on any number of numerical descriptors you have available. The program is based on maximizing the mean nearest neighbor distance in multidimensional parameter space. You have to provide an input file with all the descriptors for all the compounds in your set. The program first normalizes all the data (so that molecular weight doesn't overwhelm logP, for example). Then it selects random subsets, evaluates their similarity (using mean nearest neighbor distance), and uses a genetic algorithm to select better and better subsets. * D. Eric Walters, Ph.D., Associate Professor, Biochemistry & Molecular Biology * Finch University of Health Sciences/The Chicago Medical School * 3333 Green Bay Road, North Chicago, IL 60064 * ph 847-578-8613;fax 847-578-3240; email: Eric.Walters@finchcms.edu * "A man would do nothing if he waited until he could do it so well that * no one would find fault with what he had done." --Cardinal Newman * * * visit my web page! http://www.finchcms.edu/biochem/walters.html * * * D>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Elena, Here are two of our papers, which include a number of useful references: 1- Molecular diversity and its analysis. D. Gorse, A. Rees, M. Kaczorek and R. Lahana Drug Discovery Today, Vol.4 No. 6, June 1999. 2- Functional diversity of compound libraries. D. Gorse and R. Lahana Current Opinion in Chemical Biology, Vol.4 No.3, June 2000. Hope it helps, Roger **************************************************************** Dr Roger Lahana Synt:em Vice-President R&D Parc Scientifique G.Besse Computational Drug Discovery 30000 Nimes email: rlahana@syntem.eerie.fr France Tel: +33 (0)466 048 668 (Direct) Fax: +33 (0)466 048 667 **************************************************************** Discover New Drugs, Discover Synt:em http://www.syntem.com **************************************************************** E >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> While by no means complete, here is a list that could get you started. 1. Van Drie, J. H., Lajiness, M. S. 1998. Approaches to virtual library design. DDT 3:274-83 2. Pearlman, R. S., Smith, K. M. 1998. Software for chemical diversity in the context of accelerated drug discovery. Drugs of the Future 23:885-95 3. Hassan, M., Bielawski, J. P., Hempel, J. C., Waldman, M. 1996. Optimization and visualization of molecular diversity of combinatorial libraries. Molecular Diversity 2:64-74 4. Jamois, E. A., Hassan, M., Waldman, M. 1999. Evaluation of Reagent-Based and Product-Based Strategies in the Design of Combinatorial Library Subsets. J. Chem. Inf. Comput. Sci. 40:63-70 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121-3752 F >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to http://cisrg.shef.ac.uk and look under Recent Work for the program SELECT and accompanying references. Nick (lip97nej@sheffield.ac.uk) G >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Molecular Diversity: http://www.phar.cam.ac.uk/DDG/ Try our site and my supervisor's new book "Molecular Diversity in Drug Design (1999)" Contact him P.M.Dean@ddg.phar.cam.ac.uk if and he might be able to help. Quantitaive approaches depend on small molecule or binding site diversity. Texts on QSAR might help. James Smith _________________________________________________________________________ James Smith Drug Design Group 01223 338 600 (College) St John's College Department of Pharmacology 01223 331 985 (Office) Cambridge University of Cambridge 01223 331 740 (Fax) CB2 1TP CB2 1QJ 07625 395 084 (Pager) United Kingdom United Kingdom js252@cam.ac.uk http://www.cus.cam.ac.uk/~js252 _________________________________________________________________________ H >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I suggest you to contact Dr. Antonio Jerez, at UNED Madrid: ajerez@ccia.uned.es ***************** Julio César Llópiz Yurell IMRE, UH Zapata y G, Habana 10400, CUBA Tel (537) 781182 Fax (537) 334247 ==================================================================== --------------------------------------------------------- dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. Via Salvemini 9 I-36100 Vicenza Italy - Europe Voice ++39 0444 240341 Mobile ++39 0347 4054991 Fax ++39 0444 533954 E-mail s.in-support@mclink.it Web http://www.goldnet.it/sin/ From chemistry-request@server.ccl.net Thu Jun 1 15:33:21 2000 Received: from hermes.iupui.edu (hermes.iupui.edu [134.68.220.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA24002 for ; Thu, 1 Jun 2000 15:33:21 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by hermes.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id OAA25718; Thu, 1 Jun 2000 14:33:05 -0500 (EST) Message-ID: Date: 1 Jun 2000 14:46:41 -0500 From: "Boyd" Subject: re: similarity/diversity To: "Fioravanzo, Elena" , "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hi Elena and CCLers, Your compilation of references on molecular similarity/diversity has many articles dating from 1998 and 1999. More recent work will be published in a special double issue of the Journal of Molecular Graphics and Modelling. This journal is published in affiliation with the American Chemical Society's Computers in Chemistry division. The special issue on combinatorial library design will be released this summer. To see a list of the articles it will include, check out our website, http://chem.iupui.edu/~boyd/jmgm.html Thanks, Don Donald B. Boyd, Ph.D. Editor, Journal of Molecular Graphics and Modelling Editor, Reviews in Computational Chemistry Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd@chem.iupui.edu WWW http://chem.iupui.edu/ From chemistry-request@server.ccl.net Thu Jun 1 14:04:46 2000 Received: from mailsrv.engr.uconn.edu (mailsrv.engr.uconn.edu [137.99.21.179]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA23669 for ; Thu, 1 Jun 2000 14:04:46 -0400 Received: from engr.uconn.edu (acheniealpha [137.99.9.77]) by mailsrv.engr.uconn.edu (8.9.1a/8.9.1) with ESMTP id OAA22712 for ; Thu, 1 Jun 2000 14:04:41 -0400 (EDT) Message-ID: <3936A590.47E7D53@engr.uconn.edu> Date: Thu, 01 Jun 2000 14:04:00 -0400 From: Yuqiang Huang Organization: CAPPD_LAB To: chemistry@ccl.net Subject: Ask for kind help from one guy at Uconn. Dear Friends: I am one new Ph.D. candidate in the Dept. of Chemical Engineering at University of Connecticut. My project is "Molecular-Level Simulations of Reverse Micelles in Supercritical Carbon Dioxide for Solvent Substitution in the Chemical Industries " (designing the Surfactants for containing more water in the microemulsions to produce nanomaterials and developing a molecular-level understanding of the formation and stability of reverse micelles in supercritical carbon dioxide are two of our main points). Whould you please give me some advice about which method (such as Molecular Dynamics simulations, Monte Carlo simulations, Thermodynamic Approaches, or any other method) is good to be used fro my project? Is there any software packcage for that method and how to get it? I am expecting for your response. Your any advice is greatly appreciated! Best wishes to you, -- Yuqiang Huang ================================== Department of Chemical Engineering University of Connecticut 191 Auditorium Road, U-222 Storrs, CT 06269-3222 USA E-mail: yuqiangh@engr.uconn.edu Phone(Office): (860) 486-4600 Fax(Department): (860) 486-2959 ================================== From chemistry-request@server.ccl.net Thu Jun 1 18:15:50 2000 Received: from canter-n-siegel.schrodinger.com (canter-n-siegel.schrodinger.com [192.156.98.248]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA24688 for ; Thu, 1 Jun 2000 18:15:49 -0400 Received: (from info@localhost) by canter-n-siegel.schrodinger.com (8.8.5/8.8.5) id PAA11987 for chemistry@ccl.net; Thu, 1 Jun 2000 15:03:38 -0700 From: Schrodinger Info account Message-Id: <200006012203.PAA11987@canter-n-siegel.schrodinger.com> Subject: ANNC: Seminar on ADME Property Prediction for Real-World Problems To: chemistry@ccl.net Date: Thu, 1 Jun 2000 15:03:38 -0700 (PDT) X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Schrodinger, Inc. is pleased to announce two seminars describing our state-of-the-art tools for accurate ADME property prediction to be held on the East Coast in June. Prediction of absorption, distribution, metabolism, and excretion (ADME) properties, such as logPo/w, logS, Caco-2, and logBB, is becoming increasingly important in the process of selecting drug candidates for binding in a receptor binding pocket. Acidity and basicity can have profound effects upon chemical and physical properties. In the drug discovery process, pKa estimation plays an important role in predicting ADME properties of medicinal compounds. The seminar will illustrate key synergies among Schrodinger's software products. The first-principles based pKa Predictor in Jaguar was developed to provide accurate predictions of pKa while explicitly addressing conformational effects. A new property prediction program, QikProp (developed by Bill Jorgensen, Yale University), has both the speed and the accuracy to efficiently predict values for physically significant descriptors and pharmaceutically relevant properties of neutral organic molecules. Wednesday, June 14, 2000 9:30AM - 3:30 PM MIT - Cambridge, MA Thursday, June 22, 2000 9:30AM - 3:30 PM SGI - Parsippany, NJ If you have any questions or comments, or to register, please see our website at http://www.schrodinger.com, or contact Sharmila Pai (email: shams@schrodinger.com, phone: +1 508 628-1975). From chemistry-request@server.ccl.net Thu Jun 1 22:00:21 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id WAA25792 for ; Thu, 1 Jun 2000 22:00:03 -0400 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Fri, 02 Jun 2000 10:03:55 +0800 Sender: user@ccl.net Message-ID: <3937069F.82960802@iris.sipp.ac.cn> Date: Fri, 02 Jun 2000 09:58:07 +0900 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: thermal stability Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit Hello,everyone: I have an enzyme which I cut about ten amino acids from the wild type, and I found that the thermal stability decrease, and that means the catalytic reaction can process under the low temperature. I want to do some molecule modeling on this enzyme, does anyone have some suggetion about what I should do. Thanks in advance. Regards, mao xiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Thu Jun 1 23:17:25 2000 Received: from songsim.cuk.ac.kr ([203.229.207.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA26168 for ; Thu, 1 Jun 2000 23:17:24 -0400 Received: from songsim.cuk.ac.kr ([210.179.239.119]) by songsim.cuk.ac.kr (8.9.3/8.9.3) with ESMTP id MAA04303 for ; Fri, 2 Jun 2000 12:16:19 +0900 (KST) Message-ID: <39372765.1AA7F532@songsim.cuk.ac.kr> Date: Fri, 02 Jun 2000 12:17:57 +0900 From: young X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Dynamics analysis Content-Type: text/plain; charset=EUC-KR Content-Transfer-Encoding: 7bit Dear all I have been trying to run molecular dynamics and got some trajectory files. (*.his) Unfortunately I don't have some analysis programs for MD. I want to know or get programs that have follow tools. 1) populations vs. dihedral angles (or energy) 2) ramandranchandran plot or phi,psi map 3) Calculate for RDF or MSD Please tell me some helps. Best regards... -- ***************************************** Jee-Young Lee The Catholic University of Korea Department of Chemistry Ph.D candidate Tel. +82-32-3403-674 *****************************************