From owner-molec-model@net.bio.net Sun Jul 05 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!europa.clark.net!194.162.162.196!newsfeed.nacamar.de!univ-lyon1.fr!jussieu.fr!not-for-mail From: Michel Seigneuret Newsgroups: bionet.molec-model Subject: protein surface hydrophobicity Date: Mon, 06 Jul 1998 19:01:29 +0200 Organization: Universites Paris VI/Paris VII - France Lines: 15 Message-ID: <35A102E9.41C6@lpbc.jussieu.fr> NNTP-Posting-Host: lpbcsgi6.lpbc.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP20) Dear Collegues, I would like to use Grasp in order to display the local hydrophobicity on the molecular surface of a non-charged peptide. For this I would prefer to use atom-based rather than residue-based hydrophobicity values (e.g. as is apparently done for QSAR analysis of small molecules).Could somebody indicate me if such a method to calculate atom-based hydrophobicity parameters for proteins does exist, with reference to some publications or to an available program ? Thanks in advance. Michel Michel Seigneuret Universite Paris 6, Lab. de Physicochimie Biomoleculaire et Cellulaire 4, place Jussieu, 75252 Paris cedex 05, France From owner-molec-model@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.internetmci.com!164.67.42.145!awabi.library.ucla.edu!137.82.194.1!unixg.ubc.ca!byron!sness From: sness@FIX.TIN.DOMAIN (Steven Ness) Newsgroups: bionet.molec-model Subject: Re: protein surface hydrophobicity Date: 7 Jul 1998 18:30:41 GMT Organization: The University of British Columbia Lines: 35 Message-ID: <6ntpgh$sl7$1@nntp.ucs.ubc.ca> References: <35A102E9.41C6@lpbc.jussieu.fr> NNTP-Posting-Host: byron.biochem.ubc.ca X-Newsreader: TIN [version 1.2 PL2] Michel Seigneuret (seigneur@lpbc.jussieu.fr) wrote: : Dear Collegues, : I would like to use Grasp in order to display the local hydrophobicity : on the molecular surface of a non-charged peptide. For this I would : prefer to use atom-based rather than residue-based hydrophobicity : values (e.g. as is apparently done for QSAR analysis of small : molecules).Could somebody indicate me if such a method to calculate : atom-based hydrophobicity parameters for proteins does exist, with : reference to some publications or to an available program ? : Thanks in advance. One way that I've looked at this in Grasp is to use Grasp's excellent treatment of electrostatics and twist it into displaying hydrophobicity. The way I did this is to take Kyte-Doolittle hydrophobicity measures and equate the hydrophobicity to charge. Basically, make a new charging file that uses Kyte-Doolittle hydrophobicity spread over the atoms in each residue in some semi-intelligent way. Yeah, I know this might be considered completely bogus, but the results are not too crazy and look GREAT on the screen. We've in fact used this new hydrophobicity measure to discover some previously hidden features about proteins we've been looking at, including dimerization interfaces, active site identification and lots more. For more information and my charging file, write to me. Steven Ness sness@byron.biochem.ubc.ca Systems Assistant MP Strynadka Lab Department of Biochemistry University of British Columbia Canada From owner-molec-model@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!agate!newsfeed.wli.net!newshub.northeast.verio.net!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!dispose.news.demon.net!demon!delos!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Tim Hubbard Newsgroups: bionet.molec-model Subject: call for targets for CASP3 Date: Tue, 07 Jul 1998 13:48:23 +0100 Organization: The Sanger Centre Message-ID: <35A2190E.AC1BB650@sanger.ac.uk> Reply-To: th@sanger.ac.uk NNTP-Posting-Host: mac5.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) Lines: 268 Call for prediction targets for CASP3 ===================================== This is a call to X-ray crystallographers and NMR spectroscopists for targets for CASP3, the third experiment in critical assessment of techniques for protein structure prediction. In 1994 the first protein structure prediction experiment was held to evaluate prediction methods through blind prediction. Details of about 33 protein sequences, which were expected to be solved before the end of 1994, were submitted by experimentalists and this allowed 135 blind predictions to be made by 35 different groups. The results of the experiment are published in the November 1995 issue of Proteins: Structure, Function, and Genetics, volume 23, No 3. A second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (December 1996) was a culmination of the second 9 month long, community wide experiment. Before that meeting, 42 structural targets provided by crystallographers and NMR spectroscopists were made available to the prediction community. Prior to the public release of structures, more than 900 predictions by approximately 70 research groups world wide were collected, and led to the most objective assessment of prediction methods so far. The results are published in a special issue of Proteins: Structure, Function and Genetics, Suppl.1, 1997. The third experiment is now running and will culminate in a meeting in December 1998. As before, the goal is to obtain an in-depth and objective assessment of our current abilities and inabilities in this area. To this end, participants will predict as much as possible about a set of soon to be known structures in advance of the meeting. Sessions will be devoted to presentation of the results and comparison with experiment, and to the description of the methods used. As before, for the experiment to succeed, it is essential that we obtain the help of the experimental community. Therefore, we would like to invite Protein crystallographers and NMR spectroscopists who expect to solve a structure before 1st October 1998 to submit the sequence so that attempts can be made to predict it before it is publically announced. Each prediction will be given a deadline prior to the date on which the first information about the structure is to be made public. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold identification methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modeling methods. We would like to collect as many targets are possible. All that is requested is: - the sequence or a sequence accession number of the protein - an estimate of the likely date of public release (and updates if the work procedes faster or slower) - a commitment to make the coordinates available to the independent assessors not latter than 1st October should the structure be solved by then. Any coordinates provided will be treated with strict confidentiality as requested and used only to evalute the accuracy of predictions. For further information and on-line forms and documents see: http://predictioncenter.llnl.gov/casp3/ A Target protein submission form is also attached to this message and can be mailed to casp3@predictioncenter.llnl.gov John Moult CARB, University of Maryland, USA Tim Hubbard Sanger Centre, Hinxton, UK Jan Pedersen Acadia Pharmaceuticals, Denmark Krzysztof Fidelis Lawrence Livermore National Laboratory, USA CASP3 organising committee ---- Instructions for completing this form ------------------------------------- (0) Please only use this form if you are unable to complete the WWW version at http://predictioncenter.llnl.gov/casp3/ (1) Save this page as a text file (2) Complete all sections (3) send by email to casp3@predictioncenter.llnl.gov (4) if you have filled out the form correctly, you should receive an email acknowledgement (though not necessarily immediately) cut here ------------------------------------------------------------------------- CASP3: Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction Target submission form ====================== This is the text version of the Prediction target submission form for the Third Critical Assessment of Techniques for Protein Structure Prediction Experiment (CASP3). Introduction ============ Protein crystallographers and NMR spectroscopists are asked to provide details of structures they expect to have solved before 1st September 1998 using this form. Targets of all sizes and types are required. Small structures (less than 100 residues) are needed to test some of the ab initio structure prediction methods. Proteins with folds related to those of known structures are needed to test fold recognition methods. Proteins with sequences homologous to that of one or more known structures are needed to test comparative modelling methods. To be useful to the predictors, a period of at least a month is required before any details of the structure will be released. Please notify us immediately when the details are going to be made public, so that we can ask the predictors to stop work in a timely manner. This can be done by sending a mail to casp3@predictioncenter.llnl.gov In order for the predictions to be assessed in time for the meeting in December, we will need a set of co-ordinates by the beginning of September at the latest. If necessary, these can be for limited distribution until the meeting. A. Scientific information ========================= 1. [ ] Protein Name 2. [ ] Organism Name 3. [ ] Number of amino acids (does not need to be exact) Please provide accession number and the name of the database of the protein (4. and 5.) or the actual sequence (6.) (both if possible). 4. [ ] Accession number 5. Sequence Database [ ] Swiss-prot [ ] PIR [ ] Genbank [ ] EMBL [ ] Other [ ] 6. Amino acid sequence One letter code (ACEDFTK) is preferred, but three letter code (ala cys glu asp) can also be processed. 7. Are there homologous sequences of known structure to this protein Yes [ ] No [ ] 8. Current state of the experimental work Please describe briefly where things are at, addressing as many of the following points as you wish to/are relevant/can. The more information, the easier it is for a modeler to decide whether to predict your structure. Protein supply? Crystals? Diffraction quality? Molecular replacement in progress? Molecular replacement solution in hand? Heavy atom derivative search in progress? Heavy atom derivatives in hand? 9. Do you already have an interpretable map? Yes [ ] No [ ] 10. [ ] Estimated date of chain tracing completion. In order to assess the predictions before the meeting, this date should be before 1st September 1998. 11. [ ] Estimated date of public release of structure 12. If you have any other useful information about this sequence family please enter it below B. Administrative information ============================= 13. [ ] Name 14. Mailing address: [ ] Institution [ ] Street/P.O. Box [ ] City [ ] State/Province [ ] ZIP/Postal code [ ] Country 15. [ ] Tel 16. [ ] Fax 17. [ ] Email 18. How did you hear about this prediction experiment? [ ] Nature Add [ ] Poster [ ] Newsgroup [ ] Email [ ] Other [ ] 19. Do you wish to remain anonymous until the structure is publically announced? Yes [ ] No [ ] ------------------------------------------------------------------------- From owner-molec-model@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!BGUMAIL.BGU.AC.IL!aflaloc From: aflaloc@BGUMAIL.BGU.AC.IL (claude aflalo) Newsgroups: bionet.molec-model Subject: Re: protein surface hydrophobicity Date: 6 Jul 1998 22:55:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <35A102E9.41C6@lpbc.jussieu.fr> NNTP-Posting-Host: net.bio.net Hello Michel, On Mon, 6 Jul 1998, Michel Seigneuret wrote: > Dear Collegues, > I would like to use Grasp in order to display the local hydrophobicity > on the molecular surface of a non-charged peptide. For this I would > prefer to use atom-based rather than residue-based hydrophobicity > values (e.g. as is apparently done for QSAR analysis of small > molecules).Could somebody indicate me if such a method to calculate > atom-based hydrophobicity parameters for proteins does exist, with > reference to some publications or to an available program ? > Thanks in advance. > > Michel > > Michel Seigneuret > Universite Paris 6, Lab. de Physicochimie Biomoleculaire et Cellulaire > 4, place Jussieu, 75252 Paris cedex 05, France > I suggest you have a look at GRAMM http://reco3.musc.edu/gramm/ Hope this helps, Claude Claude Aflalo ######################## Phones: Office 972-7-6472118 #### Dept. of Life Sciences Lab 972-7-6472119 Ben Gurion University of the Negev Fax 972-7-6472890 P.O.Box 653 email: aflaloc@bgumail.bgu.ac.il Beer Sheva 84105 Israel URL: http://www.bgu.ac.il/life/aflalo.html From owner-molec-model@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!SLIP.NET!grizzly From: grizzly@SLIP.NET (Michael Sherrell) Newsgroups: bionet.molec-model Subject: Sequencers and synthesizers Date: 7 Jul 1998 14:57:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BDA9B7.B3C54080@sf-pm17-36-100.dialup.slip.net> NNTP-Posting-Host: net.bio.net I have a number of peptide and oligo synthesizers and sequencers for = sale: PerSeptive 9050, ~$10K PerSeptive Expedite 8909, <=3D $14K ABI 394, rebuilt, warranteed, Oligonet-ready, ~$12K ABI 394, rebuilt, warranteed, non-Oligonet, ~$11K ABI 391, rebuilt, warranteed, $7K ABI 430, rebuilt, warranteed, ~$12K ABI 433, rebuilt by ABI, warranteed, < $40K ABI 373 stretch, 5-filter, Genescan, 36-lane, $29K ABI 477, <=3D $10K ABI 120, 130, $2.5K also: LC-MS: Finnigan MAT 900, <$50K Finnigan MAT 90, ~$45K MicroMass Quattro II, ~$200K =09 MALDI-TOF: HP, masses to 500 KDa, lightly used, <=3D$60K Finnigan Laser MAT 2000, <$40K Other expensive hi-tech items: Bio-Dot sub-microliter 8-channel aspirate/dispense system (typically = 96-well microplate source, glass slide, microwell plate or membrane = target), < 1 year old Molecular Devices 445SI-MAC Phosphorimagers, ~ 3 years old, currently = operating and under maintenance contact, pretty low price I also have available a few other synthesizers and sequencers and a = wide selection of HPLCs, mass specs, and other lab instruments. Please contact me to discuss any of these items, or if you have any = items you might like to sell. Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com From owner-molec-model@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!howland.erols.net!vixen.cso.uiuc.edu!dhardy From: dhardy@students.uiuc.edu (david joseph hardy) Newsgroups: bionet.molec-model Subject: NAMD (parallel molecular dynamics) 1.5 beta 6 available Date: 7 Jul 1998 22:37:19 GMT Organization: University of Illinois at Urbana-Champaign Lines: 83 Message-ID: <6nu7uv$ae2$1@vixen.cso.uiuc.edu> NNTP-Posting-Host: ux9.cso.uiuc.edu Announcing the release of NAMD version 1.5 beta 6 ------------------------------------------------- The Theoretical Biophysics group at the Beckman Institute, the University of Illinois would like to announce the availability of version 1.5 beta 6 of NAMD, a high-performance molecular mechanics program for simulating large biomolecular systems on parallel and distributed computers. This software is being made available to the molecular modeling community free of charge and includes commented source code and extensive documentation. New in this version ------------------- * Enhanced performance by as much as 30%. * Modified to work with the latest version of DPMTA (2.7). * Included DPMTA source to make installation easier. * Simplified build process, fewer options to specify, better documentation. * Several bug fixes. ==================== Basic information about NAMD ====================== Obtaining NAMD -------------- A more complete description of NAMD is available on the NAMD home page: http://www.ks.uiuc.edu/Research/namd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/namd/ Email questions to namd@ks.uiuc.edu. Features -------- Efficient full electrostatics: NAMD incorporates the Distributed Parallel Multiple Tree Algorithm (DPMTA) developed by the Scientific Computing Group at Duke University to provide full electrostatic interactions in O(N) time. To further reduce the computational cost, DPMTA is integrated using a multiple timestep integration scheme which computes full electrostatic interactions only periodically during the simulation. Scalable parallelism: NAMD has an efficient parallel design that allows large systems to scale well to many processors. The use of a spatial decomposition scheme combined with message-driven execution achieves load balance and the overlap of communication and computation. Modifiable: A major design goal of NAMD is to allow researchers to implement new algorithms and techniques easily. To achieve this, NAMD design and implementation is fully documented in the NAMD Programmer's Guide. NAMD has an object-oriented design implemented in C++ to provide a high degree of modularity and data abstraction. Portable: For communication, NAMD uses PVM (Parallel Virtual Machine) from Oak Ridge National Laboratories, which has itself been ported to most architectures. Porting NAMD is then simply a matter of having PVM and a reasonable C++ compiler. We have successfully ported NAMD to all of our UNIX computers, which include HP, SGI, and Sun, both single processor and shared memory multiprocessor. Compatibility with X-PLOR: The input and output files used by NAMD are identical to those used by the program X-PLOR. Thus, simulations can be easily migrated between the two packages, allowing the output of NAMD to be analyzed using X-PLOR or any other tool built for these file formats. Standard MD features: NAMD implements standard molecular dynamics features such as energy minimization, velocity rescaling, spherical boundary conditions, harmonic constraints, and Langevin dynamics. ========================================================================== Theoretical Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign David Hardy namd@ks.uiuc.edu July 7, 1998 From owner-molec-model@net.bio.net Tue Jul 07 23:00:00 1998 From: "THX" <106213.1654@compuserve.com> Subject: software library for molecular interactions Date: Wed, 8 Jul 1998 06:35:03 +0200 Lines: 17 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Message-ID: Newsgroups: bionet.molec-model Path: biosci!pravda.ucr.edu!peerfeed.ncal.verio.net!news.idt.net!WCG!arl-news-svc-3.compuserve.com!news-master.compuserve.com!nntp-ntdwwaaw.compuserve.com Hello Our company is looking for sofwatre libraries that would compute the spacial settings between atoms when gathered. This product would be perfect if it could take into account the */- forces between atoms and steric problems. Once we have this library we want to add a 3d interface on top of it for the drug industry. Does such a product exist ? Is this newsgroup the best for such a question ? Thanks Cyril From owner-molec-model@net.bio.net Thu Jul 09 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news.maxwell.syr.edu!oleane!jussieu.fr!univ-lille1.fr!ciril.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.molec-model Subject: Re: Regular homology searches Date: 10 Jul 1998 13:37:56 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 20 Message-ID: <6o55fk$vj@news.u-strasbg.fr> References: <6o5469$r3q@mserv1.dl.ac.uk> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 Mail-Copies-To: never In article <6o5469$r3q@mserv1.dl.ac.uk>, jpleiss@tebio1.biologie.uni-stuttgart.de (Juergen Pleiss) writes: > Dear colleagues, > > We want to regularily search sequence databases for proteins which are homologous to a given target. Please take a look at DBwatcher. It is extensively used at our site, can perform both local and remote searches. It is easy to install for a wall site on a unix machine, and is free of charge. Hope this helps, François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-molec-model@net.bio.net Thu Jul 09 23:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: jpleiss@tebio1.biologie.uni-stuttgart.de (Juergen Pleiss) Newsgroups: bionet.molec-model Subject: Regular homology searches Date: 10 Jul 1998 14:15:53 +0100 Lines: 27 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6o5469$r3q@mserv1.dl.ac.uk> Original-To: jpleiss@tebio1.biologie.uni-stuttgart.de (self copy), bio-soft@dl.ac.uk, bio-www@dl.ac.uk, comp-bio@dl.ac.uk, molmodel@dl.ac.uk Dear colleagues, We want to regularily search sequence databases for proteins which are homologous to a given target. Thus, we are searching for a (commercial or academic) tool which allows us to - run a BLAST search in the current version of various protein sequence databases (SwissProt, nr,PIR,...) - mark all hits which are not yet found previously So it should - compare the results of a BLAST search with a database - create and change a database of protein sequence entries I would be glad if you could point me to such a program. Thank you for your help, Juergen Pleiss ================================================================================ Dr.Juergen Pleiss Institute of Technical Biochemistry University of Stuttgart Email:jpleiss@tebio1.biologie.uni-stuttgart.de Allmandring 31 Phone:(+49)-711-685-3191 D-70569 Stuttgart, Germany Fax: (+49)-711-685-3196 W3 home page: http://www.itb.uni-stuttgart.de:8080/ From owner-molec-model@net.bio.net Thu Jul 09 23:00:00 1998 Path: biosci!keep.out.com!spammers From: spammers@keep.out.com (Robert Fraczkiewicz) Newsgroups: bionet.molec-model Subject: New web interface to solvent accessible surface area calculations Date: 10 Jul 1998 15:29:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <35A6957C.380A2DFD@keep.out.com> NNTP-Posting-Host: net.bio.net Dear Colleagues, We would like to announce the release of beta version of GETAREA 1.0, the new free WWW service for calculating the solvent accessible surface area of molecules. Users wanting to calculate SASA of proteins will merely supply the name of their local file containing atomic coordinates in PDB format. There is an otpion to calculate solvation energy and inclusion of molecules other than proteins. The relevant URL is: http://www.scsb.utmb.edu/getarea/area_form.html Note: the current release is for testing purposes only. Surely there are still some undiscovered bugs. Please help us disclose them by submitting test inputs. All remarks and suggestions should be directed to robert@nmr.utmb.edu or werner@newton.utmb.edu Thank you in advance, Robert Fraczkiewicz Sealy Center for Structural Biology University of Texas Medical Branch Galveston, TX 77555 From owner-molec-model@net.bio.net Fri Jul 10 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!newsfeed.uk.ibm.net!ibm.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: "Ivan Torshin" Newsgroups: bionet.molec-model Subject: Exon/Intron identification Date: 11 Jul 1998 09:00:59 +0100 Organization: Kinetics and Catalysis Lab. Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6o763r$ecn@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: molmodel@dl.ac.uk Dear colleagues, Are there reliable methods of exon intron identification ( and not 'prediction') for a given protein ? Are there any databases on this subject ? Thank you, Ivan. --- From owner-molec-model@net.bio.net Sun Jul 12 23:00:00 1998 Path: biosci!CAMBRIDGE.ORG!symposia From: symposia@CAMBRIDGE.ORG (James Larkin) Newsgroups: bionet.molec-model Subject: NMR and Mass Spect Meetings Date: 13 Jul 1998 06:45:50 -0700 Organization: Cambridge Healthtech Institute Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <35AA0FE7.53B8@cambridge.org> NNTP-Posting-Host: net.bio.net I thought these two meeting might be of interest to your group NMR TECHNOLOGY: Developments and Applications October 29-30, 1998 =95 Baltimore, Maryland Advances in MASS SPECTROMETRY for Genomic and Biomolecular Research=20 January 7-8, 1999 =95 Orlando, Florida For more information please contact Cambridge Healthtech Institute 1037 Chestnut St. Newton Upper Falls, MA 02464 PH: 617-630-1300 Fax: 617-630-1325 Email: chi@healthtech.com From owner-molec-model@net.bio.net Sun Jul 12 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!europa.clark.net!206.229.87.25!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news.sprintlink.net!207.69.200.14!firehose.mindspring.net!news.mindspring.com!herwin From: herwin@gmu.edu (Harry Erwin) Newsgroups: bionet.molec-model Subject: Search Directions for Employment Date: Mon, 13 Jul 1998 08:19:06 -0400 Organization: HDE Associates Lines: 10 Message-ID: <1dc3irz.i4m4x6oiqsn4N@user-38lciqr.dialup.mindspring.com> NNTP-Posting-Host: user-38lciqr.dialup.mindspring.com X-Server-Date: 13 Jul 1998 12:20:17 GMT X-Newsreader: MacSOUP 2.3.3 My son just graduated from Antioch with a BS in biomedical sciences. His senior thesis was in computational biology--he wrote a program in C++ (the new 11/97 standard, using the STL) to compute the optimal PCR primers for an input DNA sequence. This is fairly specialized and advanced, and he has found that most employers advertising job openings in biology or chemistry are not a good fit for his skills. In what directions should he search for employment. -- Harry Erwin, herwin@gmu.edu From owner-molec-model@net.bio.net Sun Jul 12 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!chippy.visi.com!news-out.visi.com!nntp.giganews.com!news.giganews.com.POSTED!not-for-mail From: rathbun@sedona.net Newsgroups: bionet.molec-model Subject: POSITION: Product Manager/Molecular Biology Products Organization: Sedona Internet Services, Inc. Reply-To: rathbun@sedona.net X-Newsreader: Forte Free Agent 1.0.82 Lines: 88 Message-ID: Date: Mon, 13 Jul 1998 17:31:26 GMT NNTP-Posting-Host: 204.245.58.163 NNTP-Posting-Date: Mon, 13 Jul 1998 12:31:26 CDT COMPANY SUMMARY: The company is mid-sized company specializing in the development and manufacture of innovative products serving the life science research market. The company currently offers more than 2,000 products designed to facilitate gene expression and analysis, gene cloning, PRC analysis and many other molecular biology techniques used in developmental genetics, cellular biology, cancer research, antisense DNA research, genome mapping, neurobiology, oncology and several other areas. The company is very technology oriented and places great emphasis on quality, innovation, fiscal stability and responsiveness and responsibility towards customers and the community. 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JOB REQUIREMENTS Education and experience: · BA(S), MA(S), or Ph.D. in molecular biology, biochemistry, cellular biology or virology from an accredited institution either domestic U.S. or foreign with preference given to candidates with molecular biology background. · Business training or experience in product management with preference given to candidates with an MBA in a relevant discipline. · 3-5 years of technical experience in molecular biology with preference being given to candidates with directly-related work experience in companies which product molecular biology kits and reagents. · Minimum of two years of directly-relevant product management experience with preference being given to candidates with product management experience both domestic and international in scope. Knowledge and Skills Required: · Knowledge of modern molecular biology, cell biology and biochemical techniques and their use in both research and academic environments. · Good leadership and communication skills along with good analytical skills are essential. · Candidates with exceptional detail-orientation are particularly sought after. · Must possess excellent communications skills to interface with scientists both within and without the organization. This includes excellent proficiency in English (both written and verbal) and in the use of the scientific literature · Computer literacy to include operation of a Personal Computer (IBM clone and/or Mac); proficiency in the use of the Internet. · Knowledge of and experience in GMP/GLP environments. · Able to manage multiple priorities and deadlines in an expedient and decisive manner. · Must have sufficient emotional maturity and fortitude to flourish in an environment with constantly changing workloads and work requirements and must evolve with the position. If you have an interest in this or other opportunities, please send us your resume/CV as an Attached File to an email or send by mail/FAX to RS&A to the attention of Ann Rathbun, Managing Director. All correspondence is held in strict confidence. Rathbun, Sapir & Associates P.O. Box 2337 Sedona, AZ 86339-2337 * USA (520) 203-0074 Office (520) 203-0075 FAX E-mail: rathbun@sedona.net From owner-molec-model@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!spring.edu.tw!news.nctu.edu.tw!newsfeed.nthu.edu.tw!news.nthu.edu.tw!nthuls From: mjhsieh.bbs@bbs.life.nthu.edu.tw (Á©sèû) Newsgroups: bionet.molec-model Subject: Re: Use of AIX or SGI Date: 16 Jul 1998 18:23:00 GMT Organization: ²MµØ¥Í©R¬ì¾Ç BBS Lines: 8 Message-ID: <3PVRAb$Byt@bbs.life.nthu.edu.tw> NNTP-Posting-Host: bbs.life.nthu.edu.tw X-Filename: bn.mm/M.900613381.A ==> "David R. Bell" , ¬ÝªO: bn.mm wrote: : Has anyone compared AIX/RS6000 with Silicon Graphics for molecular modelling : of proteins ? : MSI software runs on both platforms, and I just wondered if either has the : edge. Can you ask the vendor list or campare their CPU performance / floating point computing power? I think it will helps. From owner-molec-model@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.internetmci.com!193.174.75.110!news-was.dfn.de!news-fra1.dfn.de!News.Uni-Marburg.DE!not-for-mail From: Marco Bocola Newsgroups: bionet.molec-model Subject: Workshop on virtual screening Date: 16 Jul 1998 06:47:15 GMT Organization: HRZ Uni Marburg Lines: 49 Message-ID: <35ADA19A.5DAC9117@mailer.uni-marburg.de> NNTP-Posting-Host: pc1661.pharmazie.uni-marburg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (WinNT; I) Dear Colleagues, we want to announce a Workshop on Virtual Screening, Schloss Rauischholzhausen, March 15-18, 1999, Germany Virtual Screening has emerged as a prospective alternative to high-throughput screening. This computer method is by no means yet mature, however it is important to seriously develop and expand its scope and to learn about its limitations. Different techniques are involved. First of all, the handling and screening of large databases that involves clustering and similarity searching. Once a reduced selection has been obtained either docking or molecular superposition methods come into play. Alternatively, libraries based on combinatorial principles from combinatorial chemistry or NMR evidence can be screened for complementarity with a given binding site or similarity with a set of given lead structures. Computational speed and reliable scoring functions either for docking or molecular superposition are essential in virtual screening. We think time is ripe to hold a workshop on this topic. The idea is to get leading experts (about 70) together at a pleasant place in a very informal atmosphere. We have reserved a castle near Marburg, about 80km from Frankfurt/M.at March 15th to 18th, 1999. If you want to know more about this meeting and you are interested to sign up please consider the web page http://pc1664.pharmazie.uni-marburg.de/workshop99/ for further information. Best regards, Hans-Joachim Boehm, Thomas Lengauer and Gerhard Klebe -- Marco Bocola Dept. of pharmaz. Chemistry AG Prof. Klebe Tel: +49-6421-28-5071 Marbacher Weg 6 Fax: -8994 D-35032 Marburg http://pc1662.pharmazie.uni-marburg.de e-mail:bocola@mailer.uni-marburg.de :-( There are no problems, just solutions !? :-) From owner-molec-model@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server1.netnews.ja.net!server2.netnews.ja.net!news.nott.ac.uk!usenet From: "David R. Bell" Newsgroups: bionet.molec-model Subject: Use of AIX or SGI Date: Thu, 16 Jul 98 19:01:21 Organization: University of Nottingham Lines: 12 Message-ID: Reply-To: "David R. Bell" NNTP-Posting-Host: ppldrbx.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Newsreader: PMINews 1.01a For OS/2 Has anyone compared AIX/RS6000 with Silicon Graphics for molecular modelling of proteins ? MSI software runs on both platforms, and I just wondered if either has the edge. Many thanks for your comments david r bell From owner-molec-model@net.bio.net Wed Jul 15 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!icet.net.nih.gov!news From: Jonathan Epstein Newsgroups: bionet.molec-model Subject: Re: Use of AIX or SGI Date: Thu, 16 Jul 1998 15:52:49 -0400 Organization: National Institutes of Health Lines: 23 Message-ID: <35AE5A11.29C4637D@nih.gov> References: NNTP-Posting-Host: 137.187.221.54 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (Win95; I) To: "David R. Bell" As I understand it, some packages such as GRASP depend upon the "GL" X extensions, and therefore only run on SGIs. I doubt that there are any modeling packages which run on AIX systems but not on SGIs. Also, since SGIs are more ubiquotous in this field, you are more likely to find pre-compiled binaries for packages of interest to you, even if they are portable to AIX. - Jonathan (speaking only for myself) David R. Bell wrote: > > Has anyone compared AIX/RS6000 with Silicon Graphics for molecular modelling > of proteins ? > > MSI software runs on both platforms, and I just wondered if either has the > edge. > > Many thanks for your comments > david r bell > > From owner-molec-model@net.bio.net Sat Jul 18 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.nyu.edu!newsfeed.sgi.net!pitt.edu!not-for-mail From: pxpst2@spam.suxs.unixs.cis.pitt.edu (Peter) Newsgroups: bionet.molec-model Subject: Re: Search Directions for Employment Date: Sun, 19 Jul 1998 12:41:35 -0500 Organization: University of Pittsburgh Lines: 31 Message-ID: References: <1dc3irz.i4m4x6oiqsn4N@user-38lciqr.dialup.mindspring.com> NNTP-Posting-Host: pelli.pathology.pitt.edu Mail-Copies-To: pxpst2@spam.suxs.unixs.cis.pitt.edu X-Newsreader: MT-NewsWatcher 2.4.4 In article <1dc3irz.i4m4x6oiqsn4N@user-38lciqr.dialup.mindspring.com>, herwin@gmu.edu (Harry Erwin) wrote: > My son just graduated from Antioch with a BS in biomedical sciences. > His senior thesis was in computational biology--he wrote a program in > C++ (the new 11/97 standard, using the STL) to compute the optimal PCR > primers for an input DNA sequence. This is fairly specialized and > advanced, and he has found that most employers advertising job openings > in biology or chemistry are not a good fit for his skills. In what > directions should he search for employment. I do not want to belittle your son's education but his project was not all that special. I have written similar routines in fortran 4 years ago. Since then, many companies have done this in their programs. So I rarely use the code I write anymore. If he wishes to do computational biology, then he will have to go back to school. To see what computational biology is like in its current state, go to www.psc.edu and look at what the biology group of Dr deerfeild is doing. If he wishes to write software then he should look at some of the "science software" vendors. As a suggestion, he should look at doing custom software or write plug-ins for freeware such as NIH image ( or other such) Peter -- "Don't you eat that yellow snow watch out where the Huskies go" FZ --------------------------------------------------------------------- From owner-molec-model@net.bio.net Sun Jul 19 23:00:00 1998 Path: biosci!elara.tripos.com!zauhar From: zauhar@elara.tripos.com Newsgroups: bionet.molec-model Subject: Re: Search Directions for Employment Date: 20 Jul 1998 14:44:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807202138.QAA11905@xhost4> NNTP-Posting-Host: net.bio.net On the contrary, with persistence Harry's son has an excellent chance of getting a job somewhere that will make good use of his skills. Not to belittle Peter's achievements in antiquated FORTRAN, four years ago lots of people were writing code for automated primer design, and some of it was fairly sophisticated. I find it hard to imagine a college senior (or anyone, for that matter) starting a project that is TOTALLY original. Although I am leaving this company to return to academia next month, if Harry will have his son send his resume here, I will see that the right people look at it. Randy All opinions expressed here are mine, not my employer's ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // \\ Tripos, Inc. | : zauhar@citroen.umsl.edu // \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // \\ St. Louis, MO 63144 | // ///////////////////////////////////////////////////////////////////////// ** ** ** "If you have conceptions of things that you can have no conception ** ** of, then the conception and the thing appear to co-incide." ** ** --- C.G. Jung ** ************************************************************************* From owner-molec-model@net.bio.net Sun Jul 19 23:00:00 1998 Path: biosci!daresbury!usenet From: Mark Faller Newsgroups: bionet.software,dl.seqnet.ccp11,dl.seqnet.general,embnet.general,dl.comp.seqnet,bionet.general,bionet.molec-model Subject: [ANNOUNCE] Fifth issue of the CCP11 newsletter is published Date: Mon, 20 Jul 1998 17:22:35 +0100 Organization: Daresbury Lab, Warrington, U.K. Lines: 28 Distribution: bionet Message-ID: <35B36EC9.EBF6D6BF@dl.ac.uk> NNTP-Posting-Host: s-ind1.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP12) Xref: biosci bionet.software:21489 bionet.general:30446 bionet.molec-model:2174 I would like to announce that the fifth issue of the CCP11 newsletter is now published. It can be found at: http://www.dl.ac.uk/CCP/CCP11/newsletter/vol2_3/ The CCP11 project is aimed at fostering the role of Bioinformatics within the British academic community. Its home page can be found at: http://www.dl.ac.uk/CCP/CCP11/ Regards, Mark. -- -------------------------------------------------------------------- | Mark Faller | E-mail: m.g.faller@dl.ac.uk | | CCP11 | Tel: +44-1925-603492 | | Daresbury Laboratory | Fax: +44-1925-603100 | | Daresbury |-----------------------------------------| | Warrington | CCP11 - Collaborative Computational | | Cheshire | Project for Biosequence and | | WA4 4AD | Structure Analysis | | United Kingdom | http://www.dl.ac.uk/CCP/CCP11/ | -------------------------------------------------------------------- From owner-molec-model@net.bio.net Mon Jul 20 23:00:00 1998 Path: biosci!WICCMAIL.WEIZMANN.AC.IL!cobogin From: cobogin@WICCMAIL.WEIZMANN.AC.IL (Oren Bogin) Newsgroups: bionet.molec-model Subject: Molecular Docking? Date: 21 Jul 1998 07:33:52 -0700 Organization: http://www.weizmann.ac.il Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <35B4D07C.74A41890@wiccmail.weizmann.ac.il> Reply-To: cobogin@wiccmail.weizmann.ac.il NNTP-Posting-Host: net.bio.net Hello I wonder if somebody could recommend a docking program (ligan-protein), that might work on PPC or PC platforms Thanks, Oren Bogin From owner-molec-model@net.bio.net Mon Jul 20 23:00:00 1998 Path: biosci!WICCMAIL.WEIZMANN.AC.IL!cobogin From: cobogin@WICCMAIL.WEIZMANN.AC.IL ("cobogin") Newsgroups: bionet.molec-model Subject: Docking programs for PPC Date: 21 Jul 1998 02:37:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello I want to be dock drugs to proteins, therefor, I want to inquire about docking programs that work preferably on PPC PC platforms. Thank you very much Oren cobogin@wiccmail.weizmann.ac.il From owner-molec-model@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: Igor.Pechersky@hboc.com Newsgroups: bionet.molec-model Subject: Re: Molecular Docking? Date: Wed, 22 Jul 1998 09:16:38 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 23 Message-ID: <6p4all$rkv$1@nnrp1.dejanews.com> References: <35B4D07C.74A41890@wiccmail.weizmann.ac.il> NNTP-Posting-Host: 208.138.70.3 X-Article-Creation-Date: Wed Jul 22 09:16:38 1998 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.01; Windows NT) In article <35B4D07C.74A41890@wiccmail.weizmann.ac.il>, cobogin@wiccmail.weizmann.ac.il wrote: > Hello > I wonder if somebody could recommend a docking program (ligan-protein), > that might work on PPC or PC platforms > Thanks, > Oren Bogin > > Try PowerFit (http://www.microsimulations.com/web0818/products/powerfit.htm), and, perhaps,"Binding of Ligands to an Infinite Linear Lattice" module for Mathematica (http://www.mathsource.com/cgi-bin/MathSource/WhatsNew/0206-031). -- Igor Pechersky, Senior Software Engineer, HBOC Medical Ltd. 8 Am veOlamo, Jerusalem 91341, Israel tel 972-2-5310244 -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-molec-model@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-nysernet-16.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!howland.erols.net!fastnet!ptdnetP!newsgate.ptd.net!news1.radix.net!tor-nx1.netcom.ca!news.cinenet.net!not-for-mail From: [psiodgf Newsgroups: bionet.molec-model Subject: -Pam Lee & Bret Michaels Sex Video...Available Now ! 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So get your credit card ready and order today. http://www.pamporn.com DMIDTEUFFUCATNGXLWDMHQETQPKXRAPBHERSBXLQ From owner-molec-model@net.bio.net Wed Jul 22 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news.maxwell.syr.edu!newsfeed.internetmci.com!24.130.1.14!lsnws01.we.mediaone.net!24.130.4.9!clnws01.we.mediaone.net.POSTED!not-for-mail Message-ID: <35B6A7BC.FFF871AB@we.mediaone.net> From: Nicolas Schoenlaub X-Mailer: Mozilla 4.5b1 (Macintosh; I; PPC) MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: ModelTrends Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Lines: 3 Date: Thu, 23 Jul 1998 03:02:44 GMT NNTP-Posting-Host: 24.130.18.178 NNTP-Posting-Date: Wed, 22 Jul 1998 20:02:44 PDT Organization: MediaOne Express, Western Region Come and visit our ModelTrends e-Magazine at http://www.modeltrends.net From owner-molec-model@net.bio.net Wed Jul 22 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-was.dfn.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Jens Erik Nielsen Newsgroups: bionet.molec-model Subject: Re: Molecular Docking? Date: Thu, 23 Jul 1998 10:44:15 +0200 Organization: EMBL Lines: 21 Distribution: world Message-ID: <35B6F7DF.32947ACF@EMBL-heidelberg.de> References: <35B4D07C.74A41890@wiccmail.weizmann.ac.il> NNTP-Posting-Host: hobby.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 5.3 IP22) Try looking at: http://cartan.gmd.de/flex-bin/FlexX I know that this thing can run under Linux. Jens Oren Bogin wrote: > > Hello > I wonder if somebody could recommend a docking program (ligan-protein), > that might work on PPC or PC platforms > Thanks, > Oren Bogin -- Jens Erik Nielsen EMBL e-mail: nielsen@embl-heidelberg.de Meyerhofstrasse 1 Tel: +49 (0) 6221 387451 69117 Heidelberg Fax: +49 (0) 6221 387517 Germany From owner-molec-model@net.bio.net Sun Jul 26 23:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Jul 1998 02:00:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807270900.CAA29175@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. 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If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-molec-model@net.bio.net Sun Jul 26 23:00:00 1998 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.molec-model Subject: What is the relation between Ea and S in the Lennard-Jones Equation? Date: 27 Jul 1998 16:52:55 GMT Organization: Vollum Lines: 18 Distribution: world Message-ID: <6pib97$eah$1@fremont.ohsu.edu> NNTP-Posting-Host: 137.53.99.50 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_PPC X-XXDate: Mon, 27 Jul 1998 17:56:41 GMT Hi all, The Lennard-Jones equation, often used in defining interaction energies in molecular modelling, expresses the Energy (E) in terms of the separation between particles and some empirical constants: E = (A/r^12) - (B/r^6). I used this to model a very simple binding reaction, and got pretty decent predictions that match experimental results. Now I'm trying to understand how the E term is related to the thermodynamic enthalpy (H) and entropy (S). The E in Lennard-Jones has the same units as H (kcal/mol for example), so is it only able to describe the enthalpic component of the reaction? How do molecular modellers deal with calculating the entropy of a simulated reaction? Thanks, Matt Jones From owner-molec-model@net.bio.net Sun Jul 26 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!news2.ais.net!jamie!ais.net!uunet!in2.uu.net!news.ici.net!not-for-mail From: "Hilton Evans" Newsgroups: bionet.molec-model Subject: ChemPen3D Software Date: 27 Jul 1998 11:14:54 GMT Organization: Chempen Software Lines: 7 Message-ID: <01bdb94f$7c9d9920$0c2ab4cf@hfevans.ici.net> NNTP-Posting-Host: d-ma-superpop-2-12.ici.net X-Newsreader: Microsoft Internet News 4.70.1162 Molecular mechanics and drawing software for Windows http://home.ici.net/~hfevans/chempen3.htm -- Hilton Evans ChemPen Chemical Structure Drawing and Modeling Software http://home.ici.net/~hfevans/chempen3d.htm From owner-molec-model@net.bio.net Sun Jul 26 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!news2.ais.net!jamie!ais.net!uunet!in2.uu.net!news.ici.net!not-for-mail From: "Hilton Evans" Newsgroups: bionet.molec-model Subject: Named Organic Reactions Date: 27 Jul 1998 11:13:57 GMT Organization: Chempen Software Lines: 7 Message-ID: <01bdb94f$5a8a2600$0c2ab4cf@hfevans.ici.net> NNTP-Posting-Host: d-ma-superpop-2-12.ici.net X-Newsreader: Microsoft Internet News 4.70.1162 200 Named Organic Reactions. More added weekly ... http://home.ici.net/~hfevans/reactions.htm -- Hilton Evans ChemPen Chemical Structure Drawing and Modeling Software http://home.ici.net/~hfevans/chempen3d.htm From owner-molec-model@net.bio.net Mon Jul 27 23:00:00 1998 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!usenet From: David Green Newsgroups: bionet.molec-model Subject: Re: What is the relation between Ea and S in the Lennard-Jones Equation? Date: Mon, 27 Jul 1998 22:23:02 -0400 Organization: Massachusetts Institute of Technology Lines: 47 Message-ID: <35BD3606.407FE3ED@lms.mit.edu> References: <6pib97$eah$1@fremont.ohsu.edu> NNTP-Posting-Host: born.lms.mit.edu Mime-Version: 1.0 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (X11; U; Linux 2.0.30 i686) Matt Jones wrote:
Hi all,

The Lennard-Jones equation, often used in defining interaction energies
in molecular modelling, expresses the Energy (E) in terms of the
separation between particles and some empirical constants: E = (A/r^12) -
(B/r^6).

I used this to model a very simple binding reaction, and got pretty
decent predictions that match experimental results. Now I'm trying to
understand how the E term is related to the thermodynamic enthalpy (H)
and entropy (S).  The E in Lennard-Jones has the same units as H
(kcal/mol for example), so is it only able to describe the enthalpic
component of the reaction? How do molecular modellers deal with
calculating the entropy of a simulated reaction?

Thanks,

Matt Jones

 The Lennard-Jones energy is the potential energy of the system, U, which is related to H by U=H-pV.  As you can see ... it doesn't consider entropy ( U in constant volume systems is somewhat analogous to H in constant pressure systems).  As for how to deal with entropy, I'm not so sure, but it depends on how large  a system your working with.  For a really small system in vacuum, you may be able to get away with calculating statistical entropy.  For larger systems, or anything in solvent, this won't work.  You might get more help if you describe your application a bit more.  For example, are you trying to do dynamics?  How big is your system, etc. 
-- 
************************************************
David F. Green
Department of Chemistry
Massachusetts Institute of Technology
77 Massachusetts Ave., Rm. 6-133
Cambridge, MA 02139

E-mail: dfgreen@lms.mit.edu
Phone: (617) 258-6229
************************************************
  From owner-molec-model@net.bio.net Mon Jul 27 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.concentric.net!howland.erols.net!Cabal.CESspool!bofh.vszbr.cz!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!csansom From: csansom@hgmp.mrc.ac.uk (Dr C Sansom) Newsgroups: bionet.molec-model,bionet.software,bionet.xtallography Subject: Modelling software: request for information Date: 28 Jul 1998 12:04:44 GMT Organization: UK HGMP Resource Centre Lines: 41 Message-ID: <6pkeos$npb$1@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: iron.hgmp.mrc.ac.uk Xref: biosci bionet.molec-model:2188 bionet.software:21540 bionet.xtallography:4328 Hello, I have been commissioned by "Nature Biotechnology" to write a short piece on the current use of software for drug design in the pharmaceutical industry. I will not be reviewing any specific programs or tools; my intention is more to talk generally about the types of software that is around and how useful it is for the particular tasks of a structure-based drug design team working in industry: specifically, target identification, homology modelling, ligand design and optimisation. I would like to represent the views of people working in companies ranging from the mega- multinationals to startup biotechs and I am particularly interested to hear from those based outside the UK. I would be very grateful if any of you were prepared to help me with this research. This would be likely to involve either a fairly short phone call or answering an email questionnaire. If you are able to help, please email me at the address below (which is *not* the address this is posted from). The deadline for the article is mid-August; many apologies for the shortness of notice. A word of advance warning: two more articles in this series are planned for later this year. These will be on, firstly, bioinformatics software and, secondly, the programs and tools used in taking a compound through pre-clinical development, clinical trials and registration. I would also be interested to know if any of you would be able to comment on the first of these, or to suggest people I could contact for the second. To fill in a little background, I am an experienced researcher in structural biology and molecular simulation, now working part time as a consultant and science writer specialising in this area. Thank you very much in advance. Best regards, Dr. Clare Sansom c.sansom@mail.cryst.bbk.ac.uk Honorary Teaching Fellow, Birkbeck College, London, UK Associate Consultant, Venus Internet Ltd., London, UK From owner-molec-model@net.bio.net Mon Jul 27 23:00:00 1998 From: "VAN DE WIELE ANNIE" Newsgroups: bionet.molec-model Subject: log P, lipophilic , hydrophic... Date: 28 Jul 1998 21:52:16 GMT Organization: NordNet, l'Internet des gens du Nord Lines: 5 Message-ID: <01bdba72$9c3810c0$caf506c3@w1> NNTP-Posting-Host: gate2-202.nordnet.fr X-Newsreader: Microsoft Internet News 4.70.1160 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!news.maxwell.syr.edu!peernews.ftech.net!ayres.ftech.net!news.ftech.net!news.intensive.net!backpost.satin.net!nordnet.fr!not-for-mail dear all, Thanks for somes weblinks about log P, about the difference between a hydrophilic group & a hydrophobic one... avandewiele@nordnet.fr From owner-molec-model@net.bio.net Tue Jul 28 23:00:00 1998 Newsgroups: bionet.molec-model,bionet.xtallography,sci.comp-aided,sci.edu,sci.techniques.xtallography,misc.education.science,bionet.molbio.proteins,alt.education.distance Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.internetmci.com!204.59.152.222!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!ucl.ac.uk!bcc.ac.uk!mail2.ccs.bbk.ac.uk!news From: software Subject: Principles of Proteins Structure '98/'99 X-Nntp-Posting-Host: cara.cryst.bbk.ac.uk Content-Type: text/plain; charset=us-ascii Message-ID: <35BEFA94.C25F87A1@mail.cryst.bbk.ac.uk> Sender: news@mail2.ccs.bbk.ac.uk Content-Transfer-Encoding: 7bit Organization: Birkbeck College, University of London, UK Mime-Version: 1.0 Date: Wed, 29 Jul 1998 10:33:57 GMT X-Mailer: Mozilla 4.05 [en] (Win95; I) Lines: 26 Xref: biosci bionet.molec-model:2190 bionet.xtallography:4331 bionet.molbio.proteins:13073 Advanced Certficate in Principles of Protein Structure '98/'99 ---------------------------------------- Dept. Crystallography, Birkbeck College, University of London. http://www.cryst.bbk.ac.uk/pps We are pleased to announce that we are now accepting registrations for this course. This award winning course is taught purely over the internet and involves a number of innovative technologies including use of BioMOO for on-line tutorials, email discussion lists, and the WWW for course material. For more information please browse the URL given above. Please send any queries/requests for application forms to Claire Burton (c.burton@mail.cryst.bbk.ac.uk). The fee for students within the European Union and countries in transition is 312 pounds sterling, for overseas self-financing students the cost is 624 pounds, and students with industrial or institutional sponsors 970 pounds. Fee payments for overseas students should be made by credit card or cheque in pounds sterling drawn on a British bank. From owner-molec-model@net.bio.net Tue Jul 28 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!news2.ais.net!jamie!ais.net!news.idt.net!nntp2.cerf.net!news.connectnet.com!not-for-mail Message-ID: <35BF6F01.5CE75B44@funtv.com> From: pmiller X-Mailer: Mozilla 4.5b1 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.molec-model,bionet.software,bionet.xtallography Subject: Re: Modelling software: request for information References: <6pkeos$npb$1@niobium.hgmp.mrc.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 47 Date: Wed, 29 Jul 1998 18:50:30 GMT NNTP-Posting-Host: 206.19.99.195 NNTP-Posting-Date: Wed, 29 Jul 1998 11:50:30 PDT Xref: biosci bionet.molec-model:2191 bionet.software:21552 bionet.xtallography:4333 Philip Miller, PhD BITS: Bioinformational Technical Services 760-944-6227 Dr C Sansom wrote: > Hello, > > I have been commissioned by "Nature Biotechnology" to write a short piece > on the current use of software for drug design in the pharmaceutical > industry. I will not be reviewing any specific programs or tools; my > intention is more to talk generally about the types of software that is > around and how useful it is for the particular tasks of a structure-based > drug design team working in industry: specifically, target identification, > homology modelling, ligand design and optimisation. I would like to > represent the views of people working in companies ranging from the mega- > multinationals to startup biotechs and I am particularly interested to > hear from those based outside the UK. > > I would be very grateful if any of you were prepared to help me with this > research. This would be likely to involve either a fairly short phone > call or answering an email questionnaire. If you are able to help, please > email me at the address below (which is *not* the address this is posted > from). The deadline for the article is mid-August; many apologies for the > shortness of notice. > > A word of advance warning: two more articles in this series are planned > for later this year. These will be on, firstly, bioinformatics software > and, secondly, the programs and tools used in taking a compound through > pre-clinical development, clinical trials and registration. I would also > be interested to know if any of you would be able to comment on the first > of these, or to suggest people I could contact for the second. > > To fill in a little background, I am an experienced researcher in > structural biology and molecular simulation, now working part time as a > consultant and science writer specialising in this area. > > Thank you very much in advance. > > Best regards, > > Dr. Clare Sansom > c.sansom@mail.cryst.bbk.ac.uk > Honorary Teaching Fellow, Birkbeck College, London, UK > Associate Consultant, Venus Internet Ltd., London, UK > From owner-molec-model@net.bio.net Tue Jul 28 23:00:00 1998 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.molec-model Subject: Re: What is the relation between Ea and S in the Lennard-Jones Equation? Date: 29 Jul 1998 19:15:41 GMT Organization: Vollum Lines: 35 Distribution: world Message-ID: <6pnsct$7i7$1@fremont.ohsu.edu> References: <6pib97$eah$1@fremont.ohsu.edu> NNTP-Posting-Host: 137.53.99.50 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_PPC X-XXDate: Wed, 29 Jul 1998 20:19:28 GMT In article <35BD3606.407FE3ED@lms.mit.edu> David Green, dfgreen@lms.mit.edu writes: > The Lennard-Jones energy is the potential energy of the system, U, >which is related to H by U=H-pV.  As you can see ... it doesn't consider >entropy ( U in constant volume systems is somewhat analogous to H in constant >pressure systems).  As for how to deal with entropy, I'm not so sure, >but it depends on how large  a system your working with.  For >a really small system in vacuum, you may be able to get away with calculating >statistical entropy.  For larger systems, or anything in solvent, >this won't work.  You might get more help if you describe your application >a bit more.  For example, are you trying to do dynamics?  How >big is your system, etc. > Thanks, that's helpful. My system is about as simple as you can get: A point "particle" representing a ligand, and two "particles" representing two parts of a protein, one is an "anchor" and is supposed to represent some large mass in the protein, and the other is a moveable "arm", supposed to represent the part of the protein that actually binds the ligand. At rest, the arm sits in the potential well generated between itself and the anchor. When the ligand is inserted nearby, the arm and the ligand generate an additional well, with a minimum at some unknown radius to be calculated. So I used Lennard-Jones as the field equation between all particles, and solved (by an optimizing algorithm) for the final positions of the particles that minimized the total system potential energy. The coefficients of the Lennard-Jones equation (radius and well-depth) and the separations between particles, were all free parameters. Now I just want to see if this has taught me anything about whether this hypothetical binding reaction is enthalpy or entropy driven, so to speak. Thanks, Matt From owner-molec-model@net.bio.net Wed Jul 29 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!newsfeed.sgi.net!pitt.edu!newsflash.concordia.ca!news.mcgill.ca!NewsWatcher!user From: uri@pharma.mcgill.ca (H. Uri Saragovi) Newsgroups: bionet.molec-model Subject: PDF available/McGill University Followup-To: bionet.molec-model Date: 30 Jul 1998 19:47:59 GMT Organization: McGill University Lines: 30 Distribution: world Message-ID: NNTP-Posting-Host: 132.206.218.126 July 30, 1998 An MRC-funded Post-Doctoral position is now available to study receptor-ligand interactions (neurotrophins and their receptors) and receptor-specific small molecule ligands. The project is amenable to study from the standpoint of cell biology, structural biology, protein engineering, drug design and development or the neurosciences. For literature examples please see : J. Neurosci 17: 6031 (1997) J. Neurosci 16:1308 (1996) Nature Biotechnology 14:1120 (1996) Jour Biol Chem 270:6564 (1995) or search other manuscripts by peruse. Expertise in any of the fields above, with a proven record of publications and achievement is required. Please reply directly at the email below. ================================ Dr. H. Uri Saragovi McGill University Pharmacology and Therapeutics and McGill Cancer Center email: uri@pharma.mcgill.ca From owner-molec-model@net.bio.net Thu Jul 30 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news.sprintlink.net!209.90.0.8!alpha.sky.net!news.missouri.edu!not-for-mail From: DS Newsgroups: bionet.molec-model Subject: Drug design. Date: Fri, 31 Jul 1998 15:38:12 -0500 Organization: University of Missouri - Columbia Lines: 15 Message-ID: <35C22B34.41C6@hamilton.math.missouri.edu> NNTP-Posting-Host: hamilton.math.missouri.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP22) I am a math graduate student and working with one of the theoretical chemist at the university here I developed a multipole algorithm for calculating coulomb interactions. With some modifications, this method can be used as a rapid screening procedure for the electrostatic version of the docking problem. The chemist that I am working with feels that this is a very important problem in the area of drug design and that I should pursue it further. In helping me to decide if I should pursue this, I was wondering if someone could briefly summarize the state of the art in this field. From owner-molec-model@net.bio.net Thu Jul 30 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!london-news-feed1.bbnplanet.com!news.bbnplanet.com!diablo.theplanet.net!dispose.news.demon.net!demon!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!loki.cf.ac.uk!not-for-mail From: fabio zuccotto Newsgroups: sci.chem,bionet.molec-model Subject: Hansch analysis Date: Fri, 31 Jul 1998 17:44:12 -0700 Organization: welsh school of pharmacy Message-ID: <35C264DC.41C6@cf.ac.uk> NNTP-Posting-Host: iris2.phrm.cf.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) Lines: 13 Hello everyone, I would like to start an Hansch or Hansch-like analysis (QSAR), I would like to know if there is any sotware available. Any comment is appreciate. Please reply to sphfz1@cf.ac.uk Thank you in advance. -- *********************************************** Fabio Zuccotto Research Student From owner-molec-model@net.bio.net Fri Jul 31 23:00:00 1998 From: "JAJansenJr" References: <35C264DC.41C6@cf.ac.uk> Subject: Re: Hansch analysis Date: Sat, 1 Aug 1998 14:07:14 -0500 Lines: 28 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.1 Message-ID: <#OjLpeXv9GA.262@upnetnews03> Newsgroups: sci.chem,bionet.molec-model NNTP-Posting-Host: 224.net7.nauticom.net [204.171.126.224] Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!207.68.152.14!upnetnews04!upnetnews03 Hello Fabio At one time I read some of the original Hansch papers. I think the most straightforward step for you to take is to decide what you want the software to do and, if there would be an advantage in having software carry out the calculations, write it yourself. Regards, Joe Jansen JAJansenJr@MSN.COM fabio zuccotto wrote in message <35C264DC.41C6@cf.ac.uk>... >Hello everyone, > >I would like to start an Hansch or Hansch-like analysis (QSAR), I would >like to know if there is any sotware available. Any comment is >appreciate. Please reply to sphfz1@cf.ac.uk > >Thank you in advance. > >-- >*********************************************** > >Fabio Zuccotto >Research Student From owner-molec-model@net.bio.net Fri Jul 31 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!la-news-feed1.bbnplanet.com!news.bbnplanet.com!newsfeed1.earthlink.net!news-ana-24.sprintlink.net!news-west.sprintlink.net!news-peer.sprintlink.net!news-nysernet-16.sprintlink.net!news.sprintlink.net!129.98.1.7!news.aecom.yu.edu!not-for-mail From: Yoram Puius Newsgroups: bionet.software.x-plor,bionet.xtallography,bionet.molec-model Subject: Simple docking Date: Sat, 01 Aug 1998 15:24:28 -0400 Organization: Dept. of Biochem., Albert Einstein Coll. of Med. Lines: 31 Message-ID: <35C36B6C.472DD50F@aecom.yu.edu> NNTP-Posting-Host: sid.bioc.aecom.yu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 6.2 IP22) Xref: biosci bionet.software.x-plor:1990 bionet.xtallography:4339 bionet.molec-model:2197 Hi all, Basic modeling question: I have a theoretical model of two docked molecules, and its godawful. However, I think that the basic binding mode is okay, so I'd like to just do some simple refinement and see if 1) I can relieve the bad contacts 2) I can get some degree of surface complementarity in the process What would be the easiest way of going about this? How hard would it be to do a rigid-body refinement in X-PLOR with the xray term off, but with vdW and electrostatics on, and how well does that work in people's experience? Do you get the molecules flying apart due to a couple of bad contacts? Alternatively, is there a better program to use? Thanks, Yoram -- _______________________________________________________________________ Yoram A. Puius Albert Einstein College of Medicine 6th year M.D.-Ph.D. Department of Biochemistry mailto:puius@aecom.yu.edu 1300 Morris Park Avenue, Bronx, NY 10461 http://www.geocities.com/Athens/Forum/7504 _______________________________________________________________________ "Naturally I have other work here, crystal structure, but often I wonder which is more useful, silly hobby or vital science." - Don DeLillo, "Ratner's Star"