From dave@carbon.chem.csiro.au Thu Jun 24 08:55:12 1993 Message-Id: <199306240355.AA10772@shark.mel.dit.csiro.au> Date: Thu, 24 Jun 93 13:55:12 EST From: (Dr.) Dave Winkler Subject: Re: GAs and conf searches To: yama@molbio.ethz.ch, chemistry@ccl.net In response to Bernhard Anton Pabsch's query on genetic algorithms, I have done some reading lately and GAs look a great way to do conformational searches. In particular, a class of GAs called "messy genetic algorithms" appear to be able to locate <> minima on energy surgfaces, something I though was essentially impossible by any means other than exhaustive systematic searches. I've queried a couple of commercial software companies and they are not looking at this. Is anyone else doing this? Cheers, Dave __________________________________________________________________________ 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. "Life is what happens to you while you're making other plans" From h.rzepa@ic.ac.uk Thu Jun 24 08:18:44 1993 Message-Id: <9306240720.AA24144@cscmgb.cc.ic.ac.uk> Date: Thu, 24 Jun 1993 08:18:44 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: CSD search >Hi, >has anybody experiences in search of hydrogen bonds >(R-O-H..OHR, intra and intermolecular) in the Cambridge >Database with output of O..H-distances and the O-H..O- >angle? > >Thanks in advance, >Andreas > This was all done by Kennard around 1982 (JACS?) using the Quest program. Version 5.5 is now available from the Cambridge Crystallographic Data centre. The user interface is standard X-windows, and the menus simple to use! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3.1, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From tennant%hau410.uk.smithkline.com@smithkline.com Thu Jun 24 12:50:48 1993 Date: Thu, 24 Jun 1993 11:50:48 +0100 (BST) From: Mike Tennant Subject: Genetic Algorithms To: chemistry@ccl.net Message-Id: Hi All! Genetic algorithms do seem 'the next step' in conformational searches, due to their seeming ability to locate global minima in reasonable amounts of time. I know of at least one group in the UK researching into conformational studies of peptides using GAs. With regard to software, there are many progs around in the public domain. The best way to find/access these, I find, is to use either gopher of wais clients. Search for 'genetic' at the veronica gopher server, and a number of servers containing GA stuff will appear!. (If you haven't got gopher, a really good search prog is xmosaic, available via anon. ftp from zaphod.ncsa.uiuc.edu in /Web/xmosaic) cheers, Mike. _____________________________________________________________________________ | _____ ____ || SmithKline Beecham Pharmaceuticals Ltd | | / ___\\\\ _ \ || Coldharbour Rd | | | |___ \\|_| | || Harlow | | \____ \ | _ < || Essex | | ___| | | |_| | || CM19 5AD | | \_____/ |____/ || England | | || Harlow (0279) 622000x3328 | |_________________________________||__________________________________________| | | | Mike Tennant | | Email: tennant%hau410.uk.smithkline.com@phinet.smithkline.com | | Email: tennantm1@smithkline.com | |*****************************************************************************| | God is real, unless declared integer. ------------------------------------------------------------------------------- From mmconn@esau.mit.edu Thu Jun 24 03:40:24 1993 Date: Thu, 24 Jun 93 07:40:24 -0400 From: mmconn@esau.mit.edu (morgan conn) Message-Id: <9306241140.AA02415@esau.mit.edu> To: chemistry@ccl.net Subject: re CSD search in response to jabs@chemie.uni-halle.d400.de who requested information on searching CSD for hydrogen bonds: Olga Kennard and Robin Taylor have done a number of studies on just this. References include: Acc. Chem. Res. 1983, 16, 146-153 (searching in general) Acc. Chem. Res. 1984, 17, 320-326 (hydrogen bond geometry) original papers: Acta Cryst. 1983, B39, 133-138 Acta Cryst. 1984, B40, 280-288 J. Am. Chem. Soc. 1984, 106, 244-248 J. Am. Chem. Soc. 1983, 105, 5761-5766 Hope this is of some help. ********************************************************* Morgan Conn MIT Chemistry, 18-148, Cambridge, MA 02139; mmconn@esau.mit.edu, 617.253.6438, 617.253.7929 (fax) ********************************************************* From Gareth.Jones@sheffield.ac.uk Thu Jun 24 13:36:48 1993 Date: Thu, 24 Jun 93 12:36:48 +0100 From: Gareth.Jones@sheffield.ac.uk (Gareth Jones) Message-Id: <9306241136.AA13521@sga.shef.ac.uk> To: CHEMISTRY@ccl.net Subject: Re: genetic algorithms for conformational search > From: (Dr.) Dave Winkler > In response to Bernhard Anton Pabsch's query on genetic algorithms, I have done > some reading lately and GAs look a great way to do conformational searches. In > From: Bernhard Anton Pabsch > Has anybody heard or applied such approach to conformational search? Hi, I've been working for the past 2 years on a phd project for Genetic Algorithms in Chemical Information Systems. One of the things I've looked at is the use of Genetic Algorithms for conformational search. A GA has been developed to search flexible molecules for pharmacophores consisting of interatomic distance patterns. A series of comparisons was undertaken by another student in our group and the GA was found to be considerably more effective than distance geometry and systematic search methods. It was, however, about half as slow as a derivative or 'directed tweak' algorithm (though this was a commercial product and I don't know if this technique could handle more complex pharmacophores with bond angles and vectors). Anyway, some of the results will be published shortly: "Searching Databases of Two-Dimensional and Three-Dimensional Chemical Structures Using Genetic Algorithms" Jones, Brown, Clark, Willett and Glen. To be presented next month at the 5th Int. Conference on GAs. Published by Morgan Kaufmann. "Pharmacophoric Pattern Matching In Files Of Three-Dimensional Chemical Structures: Comparison Of Conformational-Searching Algorithms For Flexible Searching" Clark, Jones, Willett, Glen and Kenny Presented at the 3rd Int. conference on Chemical Structures. To be published in the Journal of Chemical Information and Computer Sciences. Cheers. Gareth Jones (Gareth.Jones@sheffield.ac.uk) From dixons%phvax.dnet@smithkline.com Thu Jun 24 03:41:33 1993 Date: Thu, 24 Jun 93 07:41:33 -0400 Message-Id: <9306241141.AA03635@smithkline.com> From: dixons%phvax.dnet@smithkline.com To: "chemistry@ccl.net"%INET.dnet@smithkline.com Subject: GA applications in computational chemistry Recentley, there has been increasing interest in the application of Genetic Algorithms to computational chemistry problems. Here are some of the ones I know about (many of which are not in published form yet): A number of groups have applied GAs to protein folding type problems including Scott LeGrand and Kenny Merz at Penn State (J. Global Opt.), Shaojian Sun (Protein Science, 762, 1993), and Pat Argos (Protein Eng. 637, 1992) among others. Richard Judson (Sandia National Lab) has used GAs for conformational searching, Peter Willett at Sheffield has been using GAs for flexible 3D database searching, and I have been using GA methods for flexible docking of ligands into receptor sites. J. Blaney, D. Weiniger, and I have been working on a GA approach to de novo structure design as has Bobby Glen from Welcome. Another recent paper (E. Fontain, J. Chem. Inf, Comput Sci, 748 1992) deals with GA applications to chemical similarity. As you can see, there is a wide variety of GA applications under investigation. Some of this work has been presented at recent meetings (and I am sure I have forgotten to mention several other groups) so it is likely that a number of GA applications will be published in the near future. I think that the overall feeling is that GAs are another useful tool which, for certain types of applications can be quite valuable, but they are not the solution to all optimization problems. Some problems lend themselves to representations which work well in GAs while others do not. A good book for an introduction to Genetic Algorithms is David Goldberg, Genetic Algorithms in Search, Optimization and Machine Learning, Addison-Wesley 1989. Scott Dixon (dixons@smithkline.com) From yama@molbio.ethz.ch Thu Jun 24 16:31:50 1993 From: Bernhard Anton Pabsch Date: Thu, 24 Jun 93 14:31:50 +0200 Message-Id: <9306241231.AA22601@noldi> To: CHEMISTRY@ccl.net Subject: Structureinformations searched Dear Netters, a collegue of mine is working on C1-Esterase Inhibitor, Plasma-Kallikrein, Bradikinin and Kininogen. we search the pdb database and found 3d-struvtures of porcine kallikrein alone and complexed with bpti dating from 1984 only on the other hand sequence information searching in GCG is available in quite abundance. Now are we missing out some wellknown public informations or don't exist more published 3d structures? Also has anyone done conformational search on one of these and likes to share the coordinates? Thanks for listening bap-man ----------------------------------------------------------------------------- Bernhard A. Pabsch yama@molbio.ethz.ch Laboratorium fuer organische Chemie MOM_10@CZHETH5A.bitnet ETH Hoenggerberg (HPM G32) Tel. ++41 1 377 34 89 CH-8093 Zuerich/Switzerland Fax ++41 1 372 00 53 ----------------------------------------------------------------------------- From dok707@cvx12.inet.dkfz-heidelberg.de Thu Jun 24 18:11:23 1993 Date: Thu, 24 Jun 1993 16:11:23 +0200 From: Frank Herrmann Message-Id: <199306241411.AA12221@cvx12.inet.dkfz-heidelberg.de> To: chemistry@ccl.net Subject: RE: genetic algorithms for conformational search Hello, In response to Bernhard Anton Pabsch's query: genetic algorithms for conformational search Items: 1- references 2- special interest: codings Here the references I found so far (bibtex format): @article{photodimer, author={Marcel J. J. Blommers and Carlos B. Lucasius and Gerrit Kateman and Robert Kaptein}, title={Conformational Analysis of a Dinucleotide Photodimer with the Aid of the Genetic Algorithm}, journal={Biopolymers, Vol. 32, 45-52}, year=1992} @article{sidechains, author={P. Tuffery and C. Etchebest and S. Hazout and R. Lavery}, title={A New Approach to the Rapid Determination of Protein Side Chain Conformations}, journal={Journal of Biomolecular Structure \& Dynamics, Volume 8, Issue Number 6}, year=1991} @article{argos, author={Thomas Dandekar and Patrick Argos}, title={Potential of genetic algorithms in protein folding and protein engineering simulations}, journal={Protein Engineering vol. 5 no. 7}, pages={637-645}, year=1992} @article{teach, author={Richard S. Judson}, title={Teaching Polymers to fold}, journal={The Journal of Physical Chemistry, Vol. 96, No. 25}, year=1992} @article{grid, author={Ron Unger and John Moult}, title={genetic Algorithms for Protein Folding Simulations}, journal={Journal of Molecular Biology}, pages={75-81}, year=1993} @article{reduced, author={Shaojian Sun}, title={Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms}, journal={Protein Science}, pages={762-785}, year=1993} I am applying GA's to protein tertiary structure prediction using a SIMD massively parallel computer (MasPar). To my opinion the critical point is the coding of the conformations. When using the straightforward coding of a binary coded sequence of dihedral angles (backbone and sidechains) and an empirical force field energy as objective function, the problem seems to be GA-deceptive. I would like to contact others that work on this or a related problem to share experiences. I am especially interested in different codings for protein conformations. Regards --------------------------------------------- Frank Herrmann, Dept. of Molecular Biophysics German Cancer Research Center Im Neuenheimer Feld 280, W-6900 Heidelberg Tel: (49) 6221-422336, FAX: (49) 6221-422333 email: F.Herrmann@dkfz-heidelberg.de From markb@orl.mmc.com Thu Jun 24 08:05:09 1993 Message-Id: <9306241605.AA10668@betty> To: CHEMISTRY@ccl.net Subject: Genetic Algorithms From: markb@orl.mmc.com Date: Thu, 24 Jun 93 12:05:09 -0400 If anyone is interested in learning more about Genetic Algos and in getting some useful code, a good place to start is with the GAucsd code. The source and user's guide are both excellent and are available by anonymous ftp from cs.ucsd.edu (132.239.51.3) in the pub/GAucsd directoy. This code is becoming a defacto standard in GAs and will put you in touch with several good researchers in the field. Another promising stochastic optimization tool known as Evolutionary Programming is receiving some interest. It utilizes similar functional concepts as GAs, but takes selection as it's biological paradigm rather than genetic alleles. A good introductory article connecting EP and neural net training can be found in "Evolving Neural Netowrks", D.B.Fogel, etal, Biological Cybernetics 63, 487-493 (1990). I have been using both for pattern recognition for years and have often felt the algos would work well with the computaionally intensive energy minimization found in protein tertiary structure problems. My obstacle is a lack of data about known polypeptides/protein structures and the associated energy surfaces. I would like to use GAs/EP to predict tertiary structure if anyone knows of an accesible data location. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& "Where there is no confusion, there is no prestige." "There are no uninteresting numbers, since the first uninteresting number would be interesting." - Mathematics Made Difficult Linderholm,C.E. World Pub. 1971. From XIAO%XRAY2@ULKYVX.LOUISVILLE.EDU Thu Jun 24 08:18:10 1993 Date: Thu, 24 Jun 1993 13:18:10 -0500 (EST) From: "Leon Y. Xiao, (502)635-6931" Subject: Re: GAs and conf searches To: dave@carbon.chem.csiro.au Message-Id: <01GZR8GLETTU985B24@ULKYVX.LOUISVILLE.EDU> Hi, netters: Genetic algorithm is a powerful approach to optimization problems. Our group is currently applying GAs to intermolecular energy minimization/docking. A computer program GAME, Genetic Algorithms for Minimization of Energy, has been developed and tested on small molecular system. It seems more robust on large molecular systems than any other optimization method if used proprietly. There are quit a few research groups who applied GAs to optimization and searching related to chemistry area, of which at least one group used GAs for conformational analysis: Marcel J. J. Blommers, Carlos B. Lucasius, Gerrit Kateman, and Robert Kaptein. (1992) Biopolymers, 32, 45-52. Another group compared three global configuration search methods including GAs: R.S.Judson, M.E. Colvin, J.C.Meza, A.Huffer, and D.Gutierrez.(1992) International Journal of Quantum Chemistry, 44, 277-290. Y.L. Xiao Dr. Williams Group Department of Chemistry University of Louisville Louisville, KY 40292 (502)588-6612 xiao@xray3.chem.louisville.edu Y0XIAO01@ULKYVX.BITNET From rsjuds@california.sandia.gov Thu Jun 24 03:27:37 1993 Date: Thu, 24 Jun 93 10:27:37 -0700 From: rsjuds@ca.sandia.gov (judson richard s) Message-Id: <9306241727.AA17211@california.sandia.gov> To: chemistry@ccl.net Subject: Genetic algorithms for conformational searching Dear Netters, I and a number of collaborators have been working on the use of genetic algorithms (GAs) for conformational searching and I've also been keeping track of what other folks are doing. I think no one can guarantee that you will find the global optimum, but the method seems to find low energy conformations pretty fast. One thing to keep in mind about GAs is that they go towards minima and do not thoroughly map out the surface - If you want to know all of the local minima, GAs won't (in most cases) provide that. Here is a list of all the papers I am aware of on the subject. P. Tuffery, et al., J.Biomol. Struct. and Dyn., vol. 8, 1267 (1991) "A new approach to the rapid determination of protein side chain conformations" S. LeGrand and K. Merz, J.Global Opt. (around 1992) "The application of the Genetic Algorithm to the minimization of potential energy functions" M.J.J. Blommers, et al., Biopolymers, vol.32 45 (1992). "Conformational analysis of a dinucleotide photodimer with the aid of the genetic algorithm" R.W. Smith, Comput.Phys.Comm. (around 1992) "Energy minimization in binary alloy models via genetic algorithms" R.S. Judson, et al. Intl.J.Quant.Chem. vol 44, 277 (1992) "Do intelligent configuration search techniques outperform random search for large molecules?" R.S. Judson, J.Phys.Chem., vol 96, 10102 (1992). "Teaching polymers to fold" R. Unger and J.Moult, J.Mol.Bio. (1993) "Genetic algorithms for protein folding simulations" D.B. McGarrah and R.S. Judson, J.Comp.Chem. (December 1993) "An analysis of the genetic algorithm method of molecular conformation determination" R.S. Judson, E. Jaeger, A. Treasurywala, J.Comp.Chem. (November 1993). "Conformation searching methods for small molecules II: A Genetic algorithm approach" I hear rumors that a number of other groups are working on this in the US and Europe. ----------------------------------------------- | Richard Judson | | Center for Computational Engineering | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | (510)294-1438 | | email: rsjuds@california.sandia.gov | | | ----------------------------------------------- From jstewart@fujitsu.fai.com Thu Jun 24 05:51:30 1993 Date: Thu, 24 Jun 93 12:51:30 PDT From: jstewart@fai.com (Dr. James Stewart) Message-Id: <9306241951.AA03701@fujitsu.fai.com> To: chemistry@ccl.net Subject: MOPAC 93 and MOPAC 7 MOPAC 93 and MOPAC 7 I've received a number of E-mail messages from MOPAC users who are confused about the status of MOPAC 7 and MOPAC 93. MOPAC 7 (available from QCPE) is in the public domain. It contains all the donated code received after MOPAC 6 was released. It also contains essential bug-fixes, so that all errors which I know of which cause wrong answers have been corrected. MOPAC 7 is intended for software developers only. The quality of the code is not as good as that in MOPAC 93. MOPAC 7 should be though of as a repository of all donated code, and as such is freely available to anyone without restriction. MOPAC 93 (available from QCPE) currently runs on the SUN UNIX system only. In addition to having everything that is in MOPAC 7, it also contains my contribution, which consists of the solid state and some polishing. This code is much more robust and has better momory management than MOPAC 7. Anyone who wants can get MOPAC 93 from QCPE, and port it to their own platforms. The cost is the standard QCPE cost, but a non-redistribution agreement must be signed. Vendors are encouraged to port MOPAC 93 to their own platforms, and to make the ported version available through QCPE under the same conditions as the SUN version, that is, without a license fee or royalty. However, before the ported version can be re-distributed (i.e. sent on to QCPE), a special license is needed. Contact Miss Kumiko Iguchi, Senior Application Analyst, Fujitsu Systems Business of America, Inc., 5200 Patrick Henry Drive, Santa Clara, CA 95054; Tel: (408) 988 8012 X 226; FAX: (408) 492 1982. for more details. MOPAC 93 is the recommended program for users. It will be supported by me, and will form the basis for the next MOPAC. All donated code will be added to MOPAC 93, and when the next MOPAC is ready, the improved MOPAC 93 (MOPAC 93 with the donated code and all essential bug fixes) will be placed in the public domain. That is, the copyright will be withdrawn. James J. P. Stewart Tel: (719) 488-9416 FAX: (719) 488-9758 Email: jstewart@fai.com From mail Thu Jun 24 16:15:26 1993 Date: Thu, 24 Jun 1993 16:08:12 -0400 From: hyper!hurst (Graham Hurst) Message-Id: <9306242008.AA22771@hyper.hyper.com> To: Andy Holder , CHEMISTRY@ccl.net Subject: Re: SAM1 reference Andy Holder recently wrote: > > Hi netters. For those of you interested, Michael Dewar's new SAM1 > method now has an official reference. It is as follows: > > Dewar, M. J. S.; Jie, C.; Yu, G. Tet. 1993, 23, 5003. > > This is primarily a listing of results for the new method for a vast > array of systems. It also compares quite favorably with AM1 and > PM3. A more complete paper describing the model will be forthcoming > from my lab in the next year. Professor Dewar felt it important to > move ahead on these elements (treated without d-orbitals) because of > the superior quality of results for C, H, O, N, F, Cl, Br, and I. > We have completed work on Si and S and are beginning work on P, Fe, > and Cu. > > Thanks, Andy Holder This post disturbs me... I hope I am mistaken in concluding from the above that it will be impossible to independently reproduce these results until the "more complete paper describing the model" comes out "in the next year"! If the method has not yet been published, then the results should not have been accepted for publication since they cannot be verified. A question for Andy Holder or any of the authors of this paper: Is the SAM1 method sufficiently described in this paper (or publications it references) to allow independent verification of the reported results? If not, the SAM1 *method* still does not have an "official" reference! I eagerly await clarification... Graham ------------ Graham Hurst Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 internet: hurst@hyper.com From d3f012@pellucidar.pnl.gov Thu Jun 24 06:51:58 1993 Date: Thu, 24 Jun 93 13:51:58 -0700 From: d3f012@pellucidar.pnl.gov Subject: ****** Argus ***** To: chemistry@ccl.net Message-Id: <9306242051.AA02064@pellucidar.pnl.gov> Dear Argus users: I have been distributing Argus for about 1 year now. I would like to conduct an informal survey. The identity of all respondees will be kept private. The results of this survey will help me to identify platforms to continue to support in the future. Basically I would like to know the total number of users out there who have downloaded the program, and what hardware platform they use most often. I have had some requests for a PC version of Argus. Argus was designed and written on a PC, and has always run on that platform. I currently do not distribute a PC versions since all PC-related development/support has come from my out-of-pocket expenses. To deliver a generally useful PC version, I will have to obtain a good set of 32-bit compiler tools, etc, among other costs incurred. If there is sufficient interest, I will release a PC version. I will mail the PC version along with a hardcopy of the user manual from my home. To help defray handling costs, etc. I will have to charge a nominal cost-recovery fee. The Unix versions would continue to be distributed by anonymous ftp. I would like to find out if there is sufficient interest for me to do such a distribution. Please respond to the following by putting an "x" below as many platforms as apply to you. 1) On which platforms do you currently use Argus? (check as many as appropriate). IBM RS/6000 Sun HP SGI Cray YMP ************************************************************* 2) In addition to the above, which platforms below would you like to have supported? (check as many as appropriate). DEC AXP Cray C90 PC-compatible Macintosh Other? **************************************************************** Mark Thompson ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From CLETNER@DESIRE.WRIGHT.EDU Thu Jun 24 15:41:05 1993 Date: Thu, 24 Jun 1993 20:41:05 -0500 (EST) From: CLETNER@DESIRE.WRIGHT.EDU Subject: AMSOL program To: chemistry@ccl.net Message-Id: <01GZRPXJG1C20010D2@DESIRE.WRIGHT.EDU> Hi, I saw a posting about AMSOL. Has anybody used previous versions of this program? I am thinking that this kind of calculation could be useful but am interested in knowing it's capabilities. Ex, will it work with proteins, can you vary the solvent and composition of the solvent? Any information would be useful. Thanks Chuck Charles Letner Department of Biochem. and Mol. Bio. Wright State University Dayton, OH 45435 e-mail: cletner@desire.wright.edu For those in the MAC/PC debate: It's not the machine, it's the user. From raman@bioc01.uthscsa.edu Thu Jun 24 16:04:28 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306250204.AA01728@bioc01.uthscsa.edu> Subject: Re: genetic algorithms for conformational search To: yama@molbio.ethz.ch (Bernhard Anton Pabsch) Date: Thu, 24 Jun 1993 21:04:28 -0500 (CDT) Dear Netters Richard Judson (Sandia Research Labs) has recently published a paper entitled "Teachine Polymers to fold" (see J.Phys.Chem. 96,10102[1992]) that incorporates Genetic algorithms to do the same. It is a well written paper! In addition the following citations might prove helpful: for the new-comer: Scientific American 267, 66-72 [1992] American Scientist 80, 12-14 [1992] An overview of GA can be found in: Kybernetes 21, 26-30 [1992] Books on GA: a) Genetic Algorithms (ed) Buckles and Peky [1992] IEEE Computer society press includes reprints of articles published between 1986 - 1991 on this subject b) Genetic Algorithms and Simulated Annealing [1992] ed. Davis, L. pub: Pitman; has some nice chapters on its use in structure prediction and analysis. c) Genetic algorthms + Data Structures = evolution programs; [1992] by Z. Michalewicz, Springer Verlag Other references of interest: 1. Understanding and using GA; Chemometrics & Intell. Lab. Systems. 19,1-33 [1993] 2. Genetic algorithms for protein folding simulation ; J. Mol. Biol. 231, 75-81 [1993] 3. GA and Protein structure prediction ; Protein Science 2, 762-785 [1993] 4. Sequence assignment of 2D NMR spectra using GA; J. Chem Info and Comp. Sci. 33, 245-251 [1993] 5. Potential of GA in protein folding; work by Pat Argos; Proteins 5, 637-645 [1992] Hope this nucleates additional interest in an already exciting field!! Cheers -raman P.S. Richard Judson can be reached via email: rsjuds@sandia.llnl.gov -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************