From leclerf _-at-_)MEDCN.UMontreal.CA Tue Sep 17 10:13:15 1996 Received: from condor.CC.UMontreal.CA for leclerf %-% at %-% MEDCN.UMontreal.CA by www.ccl.net (8.7.5/950822.1) id JAA14783; Tue, 17 Sep 1996 09:19:06 -0400 (EDT) Received: from meds1.MEDCN.UMontreal.CA (meds1.MEDCN.UMontreal.CA [132.204.11.103]) by condor.CC.UMontreal.CA with ESMTP id NAA11079 (8.6.11/IDA-1.6 for ); Tue, 17 Sep 1996 13:16:54 GMT Received: from med07.MEDCN.UMontreal.CA by meds1.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id JAA10160; Tue, 17 Sep 1996 09:19:29 -0400 Received: by med07.MEDCN.UMontreal.CA (950215.SGI.8.6.10/5.17) id JAA05147; Tue, 17 Sep 1996 09:19:28 -0400 Date: Tue, 17 Sep 1996 09:19:28 -0400 From: leclerf ":at:" MEDCN.UMontreal.CA (Leclerc Fabrice) Message-Id: <9609170919.ZM5145-!at!-med07.MEDCN.UMontreal.CA> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY*- at -*www.ccl.net Subject: CCL: summary homology modeling Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters, Here is the summary concerning the validation of homology or comparative modeling methods; the original posting was: I'm looking for examples of homology modeling methods validated by the comparison between the model built and the known structure determined by = X-ray crystallography. Any reference about such examples ? ******************************Summary*************************************** On Sep 12, 8:48am, Stefan Grzybek wrote: > Subject: Re: CCL:homology modeling > On Sep 11, 6:44pm, Leclerc Fabrice wrote: > > Subject: CCL:homology modeling > > > > Dear Fabrice, > > There has been a sort of 'contest' to this subject, whose results are published > in the whole issue of Proteins Vol. 23, 1995. One of the refernces therein is > the following: > > ^%at%^ article{ 405, > AUTHOR = {{\v{S}}ali, A. and Potterton, L. and Yuan, F. and van > Vlijmen, > H. and Karplus, M.}, > TITLE = {Evaluation of Comparative Protein Modeling by {\sc Modeller}}, > JOURNAL = {Proteins}, > YEAR = {1995}, > VOLUME = {23}, > PAGES = {318--326}, > } > > Hope this helps, > Stefan > > -- > | Stefan Grzybek email: grzybek $#at#$ athena.chemie.uni-erlangen.de | > | http://athena.chemie.uni-erlangen.de/~grzybek | > | Universitaet Erlangen, Institut fuer Physikalische und Theo- | > | retische Chemie, Egerlandstr. 3, D-91058 Erlangen, Germany | > | Voice: +49 +9131 857318, Fax: +49 +9131 858307 | On Sep 12, 8:53am, Jeffrey L. Nauss wrote: > Subject: Re: CCL:homology modeling boundary > > You might look at the rubredoxins, particularly Pyrococcus furiosus. The only > two references I can grap quickly are: > > Wampler et al. Protein Science, vol 2, pages 640-649 (1993) > Bradley et al. Protein Science vol 2, pages 650-665 (1993) > > I believe the structure of Pyrococcus furiosus has been determined by X-ray > recently but I can't find the reference. A quick check of the PDB should tell > if I am mistaken. > > Looking forward to a summary as I would like to present validations in our > molecular modeling class. > > -- > Jeff Nauss > > *********************************************************************** > * UU UU Jeffrey L. Nauss, PhD * > * UU UU Director, Molecular Modeling Services * > * UU UU Department of Chemistry * > * UU UU CCCCCCC University of Cincinnati * > * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * > * UUUU CC * > * CC Telephone: 513-556-0148 Fax: 513-556-9239 * > * CC * > * CCCCCCCC e-mail: Jeffrey.Nauss ":at:" UC.Edu * > * CCCCCCC URL http://www.che.uc.edu/~nauss * > *********************************************************************** On Sep 12, 9:35am, Dick Swenson wrote: > Subject: Comp Chem Responses > Hello, > > I noted your recent query to the Computational Chemistry e-mailer regarding > the validation of homology models. You might check out the following reference > > Harrison, R.W., D. Chatterjee, and I.T. Weber. 1995. Analysis of six protein > structures predicted by comparative modeling techniques. Proteins 23:463-471. > > > Also, I have an interest in this area and would very much like to receive a > summary of any responses you get back. > > Thanks and good luck, > > Richard P. Swenson, Ph.D. > > *********************************************************************** > * Richard P. Swenson | ..... ..... . . * > * Dept of Biochemistry | Tel: 614-292-9428 . . . . . * > * Ohio State University | FAX: 614-292-6773 . . ..... . . * > * 484 West 12th Avenue | Swenson.1&$at$&osu.edu . . . . . * > * Columbus, OH 43210 | ..... .... ..... * > *********************************************************************** On Sep 12, 2:00pm, Peter Grootenhuis wrote: > Subject: homology model /xray > Dear Fabrice, we published a paper in this area in which we made a comparison > on thrombin: > Koymans, L. M. H.; Grootenhuis, P. D. J.; Haasnoot, C. A. G. > "Homology Model-building of Human Thrombin: Optimisation of Modelling > Protocol and Comparison With X-ray Structure" > Recl. Trav. Chim. Pays-Bas 1993, 112, 161-168. > Also check-out the recent paper of Moult in Curr Opin. Biotechnol. on this > subject > > Peter Grootenhuis > ______________________________________________________________________________ > Dr. Peter D.J. Grootenhuis | > N.V. Organon / CMC Dept. RK2337 | Phone : +31-412-661920 > P.O. Box 20 / 5340 BH Oss | Fax : +31-412-662539 > The Netherlands | E-mail : p.grootenhuis(+ at +)organon.akzonobel.nl > _________________________________|____________________________________________ On Sep 13, 4:40pm, Vidana C. Epa wrote: > Subject: Re: CCL:homology modeling > Hi Fabrice, > > See for example "A critical assessment of comparative molecular > modeling of tertiary structures of proteins" by S. Mosimann et al. in > Proteins, vol. 23, 301(1995). However, they don't relate the relative > success of any of the methods to any "superiority" of one method over > another. > > Cheers, > > Vidana C. Epa > > Biomolecular Research Institute, > 343 Royal Parade, > Parkville, Vic. 3052, > AUSTRALIA. > > > Tel: (61) - 3 - 9342 - 4300 > Fax: (61) - 3 - 9342 - 4301 > > email: vepa #at# tigger.mel.dbe.csiro.au > On Sep 13, 1:43pm, Mark J Forster wrote: > Subject: validation of homology modeling > > Fabrice > > Point your WWW browser to the results of the 1994 meeting on the > critical assessment of structure prediction (CASP) meeting. > http://www-bio.llnl.gov/bbrp/structural_bio/asilomar/Meeting.desc.text.html > > and see details of the upcoming CASP2 meeting > > http://iris4.carb.nist.gov/casp2/ > > > Best Wishes > > Mark J Forster > Manager Protein Applications Product Development > Molecular Simulations Inc. > 9685 Scranton Rd, > San Diego, CA 92121, USA. > Phone (619) 458 9990 > FAX (619) 458 0136 > e-mail: mjf -A_T- msi.com > WWW: http://www.msi.com/ On Sep 12, 2:12pm, Fabrice Leclerc wrote: > Subject: The current state of the art in protein structure prediction > > > > John Moult: The current state of the art in protein structure > > prediction [Review article] Current Opinion in Biotechnology 1996 7 : > > 422-427. > > > > Abstract > > The capabilities of current protein structure prediction methods have > > been assessed from the outcome of a set of blind tests. In comparative > > modeling, many of the numerical methods did not perform as well as > > expected, although the resulting structures are still of great > > practical use. The new methods of fold identification ('threading') > > were partially successful, and show considerable promise for the > > future. Except for secondary structure data, results from traditional > > ab initio methods were poor. A second blind prediction experiment is > > underway, and progress in all areas is expected. > > > > ---------------------------------------------------------------------- > > * As a registered member of BioMedNet you may read this article now > > [Full text] > > ---------------------------------------------------------------------- > > > > Electronic Press / biomednet;at;cursci.co.uk > http://BioMedNet.com/cgi-bin/members1/abstract.pl?bt7413 **********************************End of summary*******************************