From owner-molec-model@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!VEI.CO.UK!martha From: martha@VEI.CO.UK ("Martha De Souza") Newsgroups: bionet.molec-model Subject: Molecular Simulation '99 Electronic Conference Date: 2 Feb 1999 06:57:01 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 100 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.1.32.19990202152032.00924b60@proteus.vei.co.uk> NNTP-Posting-Host: net.bio.net Applications and Methodology of Molecular Simulation ---------------------------------------------------- in the Physical and Biological Sciences ---------------------------------------------------- -- An International Conference in Electronic Format -- sponsored by Gordon and Breach Conference Chair: Professor Nick Quirke, Imperial College, Editor-in-Chief, Molecular Simulation Journal Dates: 19 April - 4 May '99 URL: http://molsim.vei.co.uk/ ___________________________________________________________ ** Now calling for PAPERS - Submit your abstract via the on-line form at http://molsim.vei.co.uk/submissions/index.html N.B. Deadline for abstracts = 1 March 1999 ** FREE Registration to attend the conference now available - Fill in the form at http://molsim.vei.co.uk/register/index.html ____________________________________________________________ ___DESCRIPTION___ The international journal Molecular Simulation is sponsoring a virtual conference on the latest applications and techniques in the field. The conference will bring together experts, in a wide range of disciplines encompassed within the physical and biological sciences, using molecular simulation and related techniques. An important aim of the meeting is to foster cross fertilisation of ideas, algorithms and applications between them. Sessions will include papers on topics in physics, chemistry, materials science, biology and pharmacology. Comment and discussion will be encouraged and the resulting material will be edited and form part of the proceedings. The format of the virtual conference will be formal sessions with invited and contributed papers, posters and subsequent interactive discussions with authors, where comment and criticism will be sought on the formal lectures (along the lines of a Faraday Discussion). During the conference all material will be accessible at the conference Web site and accepted papers will be published after the end of the conference (following refereeing and editing) in Molecular Simulation. ___TOPICS, CHAIRS and SPEAKERS___ The six sections will cover the following topics. Also find listed the chairs for each topic and some of the invited speakers confirmed so far. Applications: 1. Frontiers of Materials Science Chairs: Prof. Alain Fuchs, Prof. C R A Catlow Invited Speakers: 2. Novel Applications in Chemistry and Physics Chairs: Prof Donald Brenner, Dr. Deepak Srivastava Invited Speakers: 3. Computer based Modelling, Simulation, and Analysis of Biological and Pharmacological Systems Chairs: Prof. Graham Richards, Dr. Jeffrey L. Nauss Invited Speakers: Steve Doughty, Vijay Gombar, Ian Haworth, Prof. Mati Karelson, Dave Winkler Methodology: 4. Advances in Mesoscale Simulation Methodology Chairs: Dr. Julia Yeomans, Dr. Dave Nicolaides Invited Speakers: Bruce Boghosian, Hudong Chen, J.G.E.M. Fraaije, Anatoly Malevanets 5. Non Equilibrium and Monte Carlo Simulation Chairs: J.M.D.MacElroy, B.E.Ph.D., Grant S. Heffelfinger, Ph.D. Invited Speakers: Prof. David M. Ford, Prof. Akira Miyamoto, Dr. David Nicholson, Prof. Tomoshige Nitta, Dr. Aidan Thompson, Dr. Karl P. Travis, 6. Advances in Quantum Simulation Chairs: Dr. Dominic King-Smith, Dr. M.C. Payne Invited Speakers: Mike Gillan, Pablo Ordejon, Dr. Mike Payne, Gustavo Scuseria, Alain St-Amant ____________________________________________________________________________ ___________________________________ I hope that this conference will be of interest to some people on the list. I apologise for any duplicate postings received by people subscribed to other lists. Yours sincerely, Martha de Souza VEI martha@vei.co.uk From owner-molec-model@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!feed1.news.rcn.net!rcn!newsfeed.cwix.com!194.72.7.126!btnet-peer!btnet-feed1!btnet!news-reader.bt.net!news1lo.highwayone.net!62.232.8.53 Message-ID: <36B6ED24.5078BBBE@vei.co.uk> From: Martha De Souza Organization: VEI X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: Molecular Simulation '99 Electronic Conference Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 103 Date: Tue, 02 Feb 1999 12:18:44 +0000 NNTP-Posting-Host: 195.70.64.24 X-Trace: news-reader.bt.net 917956221 195.70.64.24 (Tue, 02 Feb 1999 11:50:21 BST) NNTP-Posting-Date: Tue, 02 Feb 1999 11:50:21 BST Applications and Methodology of Molecular Simulation in the Physical and Biological Sciences -------------------------------------------------------------------------------------------- -- An International Conference in Electronic Format sponsored by Gordon and Breach -- Conference Chair: Professor Nick Quirke, Imperial College, Editor-in-Chief, Molecular Simulation Journal Dates: 19 April - 4 May '99 URL: http://molsim.vei.co.uk/ _________________________________________________________________________________ ** Now calling for PAPERS - Submit your abstract via the on-line form at http://molsim.vei.co.uk/submissions/index.html N.B. Deadline for abstracts = 1 March 1999 ** FREE Registration to attend the conference now available - Fill in the form at http://molsim.vei.co.uk/register/index.html _________________________________________________________________________________ ___DESCRIPTION___ The international journal Molecular Simulation is sponsoring a virtual conference on the latest applications and techniques in the field. The conference will bring together experts, in a wide range of disciplines encompassed within the physical and biological sciences, using molecular simulation and related techniques. An important aim of the meeting is to foster cross fertilisation of ideas, algorithms and applications between them. Sessions will include papers on topics in physics, chemistry, materials science, biology and pharmacology. Comment and discussion will be encouraged and the resulting material will be edited and form part of the proceedings. The format of the virtual conference will be formal sessions with invited and contributed papers, posters and subsequent interactive discussions with authors, where comment and criticism will be sought on the formal lectures (along the lines of a Faraday Discussion). During the conference all material will be accessible at the conference Web site and accepted papers will be published after the end of the conference (following refereeing and editing) in Molecular Simulation. ___TOPICS, CHAIRS and SPEAKERS___ The six sections will cover the following topics. Also find listed the chairs for each topic and some of the invited speakers confirmed so far. Applications: 1. Frontiers of Materials Science Chairs: Prof. Alain Fuchs, Prof. C R A Catlow Invited Speakers: 2. Novel Applications in Chemistry and Physics Chairs: Prof Donald Brenner, Dr. Deepak Srivastava Invited Speakers: 3. Computer based Modelling, Simulation, and Analysis of Biological and Pharmacological Systems Chairs: Prof. Graham Richards, Dr. Jeffrey L. Nauss Invited Speakers: Steve Doughty, Vijay Gombar, Ian Haworth, Prof. Mati Karelson, Dave Winkler Methodology: 4. Advances in Mesoscale Simulation Methodology Chairs: Dr. Julia Yeomans, Dr. Dave Nicolaides Invited Speakers: Bruce Boghosian, Hudong Chen, J.G.E.M. Fraaije, Anatoly Malevanets 5. Non Equilibrium and Monte Carlo Simulation Chairs: J.M.D.MacElroy, B.E.Ph.D., Grant S. Heffelfinger, Ph.D. Invited Speakers: Prof. David M. Ford, Prof. Akira Miyamoto, Dr. David Nicholson, Prof. Tomoshige Nitta, Dr. Aidan Thompson, Dr. Karl P. Travis, 6. Advances in Quantum Simulation Chairs: Dr. Dominic King-Smith, Dr. M.C. Payne Invited Speakers: Mike Gillan, Pablo Ordejon, Dr. Mike Payne, Gustavo Scuseria, Alain St-Amant _______________________________________________________________________________________________________________ I hope that this conference will be of interest to some people on the list. I apologise for any duplicate postings received by people subscribed to other lists. Yours sincerely, Martha de Souza VEI martha@vei.co.uk From owner-molec-model@net.bio.net Mon Feb 01 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!isdnet!oleane!jussieu.fr!moka.ccr.jussieu.fr!not-for-mail From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN) Newsgroups: bionet.molec-model Subject: minimal sphere Date: 2 Feb 1999 15:42:05 +0100 Organization: CCR - Universites Paris VI/VII - Paris - France Lines: 15 Message-ID: <7972rt$31ca@moka.ccr.jussieu.fr> NNTP-Posting-Host: moka.ccr.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Subj: minimal sphere A colleague told me recently that it should be useful to have a programme computing the minimal sphere containing a molecule, together with various shape coefficients. I have done it. Binaries are available for DEC-alpha (VMS and unix), RS6000 serie (and SP2) CRAY Y and J90, SGI O2 (and various mips1 to mips4). Interested people should email me, without forgetting to tell which computer is used. Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, ESA 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 01 44 27 48 57 75005 Paris, France. FAX : +33 01 45 84 98 25 From owner-molec-model@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!newscore.univie.ac.at!aconews.univie.ac.at!news.univie.ac.at!not-for-mail From: Herbert Plass Newsgroups: bionet.molec-model Subject: Proteins 3D Date: Wed, 03 Feb 1999 08:01:55 GMT Organization: Vienna University, Austria Lines: 15 Message-ID: <19990203.8015500@plass.pharm.univie.ac.at> Reply-To: herbert.plass@univie.ac.at NNTP-Posting-Host: plass.pharm.univie.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable X-Trace: www.univie.ac.at 918029017 114940 131.130.53.24 (3 Feb 1999 08:03:37 GMT) X-Complaints-To: news-adm@news.univie.ac.at NNTP-Posting-Date: 3 Feb 1999 08:03:37 GMT X-Priority: 3 (Normal) X-Newsreader: Mozilla/3.0 (compatible; StarOffice/5.0; Unix) Hallo! I am looking for software (for Linux) to generate those nice pictures=20 with ribbons and tubes ... for proteins. i.e. tertiary (and=20 quarternary?) structures. I tried to start with those expasy programs,=20 but failed, because there is no model structure available for my=20 protein. Hence there shold be a prediction program, which uses the AS=20 sequence. Thanks Herbert Plass University Vienna, Austria From owner-molec-model@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!newscore.univie.ac.at!aconews.univie.ac.at!news.univie.ac.at!not-for-mail From: Herbert Plass Newsgroups: bionet.molec-model Subject: Re: Proteins 3D Date: Wed, 03 Feb 1999 13:52:14 GMT Organization: Vienna University, Austria Lines: 32 Message-ID: <19990203.13521400@plass.pharm.univie.ac.at> References: <19990203.8015500@plass.pharm.univie.ac.at> Reply-To: herbert.plass@univie.ac.at NNTP-Posting-Host: plass.pharm.univie.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable X-Trace: www.univie.ac.at 918050035 70206 131.130.53.24 (3 Feb 1999 13:53:55 GMT) X-Complaints-To: news-adm@news.univie.ac.at NNTP-Posting-Date: 3 Feb 1999 13:53:55 GMT X-Priority: 3 (Normal) X-Newsreader: Mozilla/3.0 (compatible; StarOffice/5.0; Unix) >>>>>>>>>>>>>>>>>> Urspr=FCngliche Nachricht <<<<<<<<<<<<<<<<<< Am 03.02.99, 10:53:34, schrieb m.mitchell@icrf.icnet.uk (Mike=20 Mitchell) zum Thema Re: Proteins 3D: > herbert.plass@univie.ac.at wrote: > > I am looking for software (for Linux) to generate those nice picture= s > > with ribbons and tubes ... for proteins. i.e. tertiary (and > > quarternary?) structures. I tried to start with those expasy program= s, > > but failed, because there is no model structure available for my > > protein. Hence there shold be a prediction program, which uses the A= S > > sequence. > Try using SwissModel to predict the structure, the results are=20 returned > as a PDB format file. PDB files can be "rendered" as ribbons and tubes= > with applications such as RasMol. Thank you, what I meant with _expasy programs_ was actually SwissModel. But I=20 understood, that for a prediction this program needs some kind of=20 template. When I submitted the query for my sequence, i got the=20 answer, that there is no model and hence therefore a calculation is=20 impossible. I would be glad if I am wrong and there _is_ a way to=20 calculate a guess. Herbert Plass From owner-molec-model@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newspeer.monmouth.com!rill.news.pipex.net!pipex!uu.fr!imaginet.net!imaginet.fr!usenet From: "vermeim" Newsgroups: bionet.molec-model Subject: Int Sympo Molecular Genetics of Mental Disorders Date: Wed, 3 Feb 1999 13:28:26 +0100 Organization: ImagiNET Lines: 9 Message-ID: <799emh$3kg$1@news.imaginet.fr> NNTP-Posting-Host: 195.68.9.163 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 International Symposium "Molecular Genetics of Mental Disorders" Date : December 1-3, 1999 Castres (Tarn) France The final scientific program is now available on http://www.entretiens-du-carla.com From owner-molec-model@net.bio.net Tue Feb 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!diablo.theplanet.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!m.mitchell From: m.mitchell@icrf.icnet.uk (Mike Mitchell) Newsgroups: bionet.molec-model Subject: Re: Proteins 3D Date: Wed, 03 Feb 1999 09:53:34 +0000 Organization: Imperial Cancer Research Fund Lines: 34 Message-ID: References: <19990203.8015500@plass.pharm.univie.ac.at> NNTP-Posting-Host: morpheus.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 In article <19990203.8015500@plass.pharm.univie.ac.at>, herbert.plass@univie.ac.at wrote: > Hallo! > > I am looking for software (for Linux) to generate those nice pictures > with ribbons and tubes ... for proteins. i.e. tertiary (and > quarternary?) structures. I tried to start with those expasy programs, > but failed, because there is no model structure available for my > protein. Hence there shold be a prediction program, which uses the AS > sequence. Try using SwissModel to predict the structure, the results are returned as a PDB format file. PDB files can be "rendered" as ribbons and tubes with applications such as RasMol. SwissModel (web): http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html RasMol: http://www.glaxowellcome.co.uk/science/software/ ftp://ftp.dcs.ed.ac.uk/pub/rasmol/ There are several other applications that can display PDB data. -- Michael Mitchell "Smoke me a kipper, User Support I'll be back for breakfast." Molecular Biology Software Ace Rimmer, Test Pilot +44 (0)171 269 3115 BBC-TV Red Dwarf ENFJ From owner-molec-model@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.metronet.de!uni-erlangen.de!news-nue1.dfn.de!news-lei1.dfn.de!news-ber1.dfn.de!news.uni-potsdam.de!newsadm From: "Frank Fürst" Newsgroups: bionet.molec-model Subject: Re: Proteins 3D Date: Wed, 03 Feb 1999 18:08:20 +0100 Organization: University of Potsdam Lines: 43 Message-ID: <36B88284.5542D204@rz.uni-potsdam.de> References: <19990203.8015500@plass.pharm.univie.ac.at> <19990203.13521400@plass.pharm.univie.ac.at> NNTP-Posting-Host: pc207-60.biochem.uni-potsdam.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.06 [de]C-QXW0310E (Win95; I) To: herbert.plass@univie.ac.at Herbert Plass schrieb: > >>>>>>>>>>>>>>>>>> Ursprüngliche Nachricht <<<<<<<<<<<<<<<<<< > > > I am looking for software (for Linux) to generate those nice pictures > > > with ribbons and tubes ... for proteins. i.e. tertiary (and > > > quarternary?) structures. I tried to start with those expasy programs, > [...] > answer, that there is no model and hence therefore a calculation is > impossible. I would be glad if I am wrong and there _is_ a way to > calculate a guess. > > Herbert Plass Hi, I hope you know that calculating "those nice pictures with ribbons and tubes", i.e. calculating the protein structure, without any model or without structural (X-ray, NMR) data of your protein is a _very_ difficult thing? If it was possible for every protein, a whole bunch of scientists would be both happy and unemployed. Surely there are algorithms, and sometimes they work quite fine, but sometime the same algorithm doesn't work at all on a particular protein, or predicts a structure which is later, by the use of experimental (X-ray, NMR) data shown to be wrong, or at least not completely right. A prominent example which may be known by other people than structural biologists is the predicted and NMR-structure of the [hamster]prion protein [NMR: Wuethrich, Glockshuber et al., somewhen in 1997, I think in Nature]. So if you find a prediction program and pass your aa-sequence through it, it might be you get some structure, but you'll have to be extremely careful in interpreting it, especially if you're not an expert in that field. In my opinion it would be better to admit that you don't know the structure and not show any, instead of presenting a guess which might be good, or bad. btw I think that there exist methods of elucidating the structure of a binding site by NMR if you know the conformation of a (non-macromolecular?) ligand, which would be easier than doing the whole structure. Ask a pharmacologist. Frank From owner-molec-model@net.bio.net Wed Feb 03 22:00:00 1999 Message-ID: <36B952D2.50DA09BA@came.sbg.ac.at> Date: Thu, 04 Feb 1999 08:57:06 +0100 From: Walter Koppensteiner Organization: Center for Applied Molecular Engineering X-Mailer: Mozilla 4.5C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en,de MIME-Version: 1.0 Newsgroups: bionet.molec-model To: herbert.plass@univie.ac.at Subject: Re: Proteins 3D References: <19990203.8015500@plass.pharm.univie.ac.at> <19990203.13521400@plass.pharm.univie.ac.at> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit NNTP-Posting-Host: agnes.came.sbg.ac.at Lines: 55 Path: biosci!agate!newsfeed.berkeley.edu!europa.clark.net!192.174.65.44!newscore.univie.ac.at!newsfeed03.univie.ac.at!news.sbg.ac.at!agnes.came.sbg.ac.at Herbert Plass wrote: > > >>>>>>>>>>>>>>>>>> Ursprüngliche Nachricht <<<<<<<<<<<<<<<<<< > Am 03.02.99, 10:53:34, schrieb m.mitchell@icrf.icnet.uk (Mike > Mitchell) zum Thema Re: Proteins 3D: > > herbert.plass@univie.ac.at wrote: > > > I am looking for software (for Linux) to generate those nice pictures > > > with ribbons and tubes ... for proteins. i.e. tertiary (and > > > quarternary?) structures. I tried to start with those expasy programs, > > > but failed, because there is no model structure available for my > > > protein. Hence there shold be a prediction program, which uses the AS > > > sequence. > > > Try using SwissModel to predict the structure, the results are > returned > > as a PDB format file. PDB files can be "rendered" as ribbons and tubes > > with applications such as RasMol. > > Thank you, > what I meant with _expasy programs_ was actually SwissModel. But I > understood, that for a prediction this program needs some kind of > template. When I submitted the query for my sequence, i got the > answer, that there is no model and hence therefore a calculation is > impossible. I would be glad if I am wrong and there _is_ a way to > calculate a guess. > > Herbert Plass You can try to predict a model of this protein using fold recognition. This method is very successful in many cases and its applicability was demonstrated in a public blind prediction test (CASP3): http://PredictionCenter.llnl.gov/casp3/Casp3.html. We participated in CASP3 and our fold recognition program was quite successful. The Web page of this program is redesigned at the moment and therefore not accessible (I can send you the Web address as soon as the page is available again.) There is not guarantee to find a template for every sequence but the chances are rather good because the number of folds in the PDB is already quite large. Hope this helps, Walter -- =============================================================== Walter Koppensteiner University of Salzburg Center of Applied Molecular Engineering Jakob Haringer Strasse 3 Phone: +43-662-8044-5794 A-5020 Salzburg, Austria Fax: +43-662-454889 Email: walter@came.sbg.ac.at =============================================================== From owner-molec-model@net.bio.net Wed Feb 03 22:00:00 1999 Path: biosci!YAHOO.COM!dureti3 From: dureti3@YAHOO.COM Newsgroups: bionet.molec-model Subject: (none) Date: 4 Feb 1999 11:45:31 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 67 Sender: daemon@net.bio.net Distribution: world Message-ID: <199902041945.LAA27891@net.bio.net> NNTP-Posting-Host: net.bio.net We'll Submit Your Site To Over 900 Search Engines, Directories, & Indices For A "One Time Cost" Of Only $ 39.95 *** 100% Money Back Guarantee *** *** Immediately Increase Your Sites Exposure *** For Less Than 4 Cents Each We Will Submit Your Web Site To Over 900 Of The Net's Hottest Search Engines, Directories & Indices. If your site isn't listed in the Search Engines, how can people find you to buy your products or services? For just $39.95 we'll take the work load off your back instead of you trying to do it manually which can take days to do. We're the professionals that are here to help you have a shot at having a successful marketing experience with the internet. You know as well as we that your time is best utilized managing your business and not sitting at some keyboard hours upon hours trying to save less than 4 cents for each submission. See how it's kind of crazy to try to tackle this on your own. It's just not cost effective to try to do this yourself to save just $39.95. See why thousands and thousands of businesses world wide both large and small have come to us to utilize our services. Hotels, Motels, On-Line Stores, Travel Agents, Colleges, Universities, Governments, Fortune 500 companies, Movie Studios, Chambers Of Commerce and many, many more. Shouldn't you give us a call now? To Learn More, Call Us At The Numbers Below. Call us toll free at (800) 771-2003 in the USA and Canada or outside the USA at (916) 771-4739 and we'll provide you with all the necessary information to get you submitted Right Away. #2488 To be removed from our mailing list, please respond with the word remove in the subject. From owner-molec-model@net.bio.net Mon Feb 08 22:00:00 1999 Path: biosci!ATC.ATCCU.CHULA.AC.TH!porn From: porn@ATC.ATCCU.CHULA.AC.TH Newsgroups: bionet.molec-model Subject: Bioinformatic: need help! Date: 8 Feb 1999 22:39:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Sir, We are going to organize the symposium on the computation science and engeering. Bioinformatic is one of the main topic that we would like to include. The subjects should focus on the basic research that can eventually apply to the industry. But we are not sure whether our aim would be possible or not. Thus, we are looking for these information. We will appreciate if anyone could kindly provide any comments. Thank you in advance. Thep ************************************ Dr.Pornthep Sompornpisut Faculty Staff Faculty of Science Chulalongkorn University Bangkok Thailand Tel: 66-2-2185222 Fax: 66-2-2521730 e-mail:spornthe@atc.atccu.chula.ac.th ************************************ From owner-molec-model@net.bio.net Wed Feb 10 22:00:00 1999 Path: biosci!news.stanford.edu!news.ems.psu.edu!news.cis.ohio-state.edu!malgudi.oar.net!hyperion.wright.edu!news.wright.edu!not-for-mail From: Deacon Sweeney Newsgroups: bionet.molec-model Subject: Re: Proteins 3D Date: Tue, 09 Feb 1999 19:05:21 -0500 Organization: Wright State University Lines: 59 Message-ID: <36C0CD41.167E@wright.edu> References: <19990203.8015500@plass.pharm.univie.ac.at> <19990203.13521400@plass.pharm.univie.ac.at> <36B88284.5542D204@rz.uni-potsdam.de> NNTP-Posting-Host: linus.bmb.wright.edu Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) Frank Fürst wrote: > > Herbert Plass schrieb: > > > >>>>>>>>>>>>>>>>>> Ursprüngliche Nachricht <<<<<<<<<<<<<<<<<< > > > > I am looking for software (for Linux) to generate those nice pictures > > > > with ribbons and tubes ... for proteins. i.e. tertiary (and > > > > quarternary?) structures. I tried to start with those expasy programs, > > > > [...] > > > answer, that there is no model and hence therefore a calculation is > > impossible. I would be glad if I am wrong and there _is_ a way to > > calculate a guess. > > > > Herbert Plass > > Hi, > I hope you know that calculating "those nice pictures with ribbons and tubes", > i.e. calculating the protein structure, without any model or without > structural (X-ray, NMR) data of your protein is a _very_ difficult thing? > If it was possible for every protein, a whole bunch of scientists would be > both happy and unemployed. Surely there are algorithms, and sometimes they > work quite fine, but sometime the same algorithm doesn't work at all on a > particular protein, or predicts a structure which is later, by the use of > experimental (X-ray, NMR) data shown to be wrong, or at least not completely > right. A prominent example which may be known by other people than structural > biologists is the predicted and NMR-structure of the [hamster]prion protein > [NMR: Wuethrich, Glockshuber et al., somewhen in 1997, I think in Nature]. > > So if you find a prediction program and pass your aa-sequence through it, it > might be you get some structure, but you'll have to be extremely careful in > interpreting it, especially if you're not an expert in that field. > In my opinion it would be better to admit that you don't know the structure > and not show any, instead of presenting a guess which might be good, or bad. > > btw I think that there exist methods of elucidating the structure of a binding > site by NMR if you know the conformation of a (non-macromolecular?) ligand, > which would be easier than doing the whole structure. Ask a pharmacologist. > > Frank Herbert, Frank is right. To exemplify, I read in a not to far past Biophysical Journal, that, even with simplified, shortened sequences (<20aa) it was difficult for some experts to make a computer fold alpha-helices by strict algorithms. Even these weren't all that close to emperical observation. How big is your protein, and what is it's name? If you can find an ancestor close enough (>50% homology); mutate it, minimize the energy, and send it through molecular dynamics, and you _might_ have a good guess. This can all be done with Tripos' SYBYL. Let us know how things work out. Deacon Sweeney Wright State University From owner-molec-model@net.bio.net Wed Feb 10 22:00:00 1999 Path: biosci!mh.us.sbphrd.com!bowermj From: bowermj@mh.us.sbphrd.com ("Michael J. Bower") Newsgroups: bionet.molec-model Subject: Re: Proteins 3D Date: 11 Feb 1999 05:18:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 86 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net >Frank Fürst wrote: >> >> Herbert Plass schrieb: >> >> > >>>>>>>>>>>>>>>>>> Ursprüngliche Nachricht <<<<<<<<<<<<<<<<<< >> > > > I am looking for software (for Linux) to generate those nice pictures >> > > > with ribbons and tubes ... for proteins. i.e. tertiary (and >> > > > quarternary?) structures. I tried to start with those expasy programs, >> > >> >> [...] >> >> > answer, that there is no model and hence therefore a calculation is >> > impossible. I would be glad if I am wrong and there _is_ a way to >> > calculate a guess. >> > >> > Herbert Plass >> >> Hi, >> I hope you know that calculating "those nice pictures with ribbons and tubes", >> i.e. calculating the protein structure, without any model or without >> structural (X-ray, NMR) data of your protein is a _very_ difficult thing? >> If it was possible for every protein, a whole bunch of scientists would be >> both happy and unemployed. Surely there are algorithms, and sometimes they >> work quite fine, but sometime the same algorithm doesn't work at all on a >> particular protein, or predicts a structure which is later, by the use of >> experimental (X-ray, NMR) data shown to be wrong, or at least not completely >> right. A prominent example which may be known by other people than structural >> biologists is the predicted and NMR-structure of the [hamster]prion protein >> [NMR: Wuethrich, Glockshuber et al., somewhen in 1997, I think in Nature]. >> >> So if you find a prediction program and pass your aa-sequence through it, it >> might be you get some structure, but you'll have to be extremely careful in >> interpreting it, especially if you're not an expert in that field. >> In my opinion it would be better to admit that you don't know the structure >> and not show any, instead of presenting a guess which might be good, or bad. >> >> btw I think that there exist methods of elucidating the structure of a binding >> site by NMR if you know the conformation of a (non-macromolecular?) ligand, >> which would be easier than doing the whole structure. Ask a pharmacologist. >> >> Frank > >Herbert, > > Frank is right. To exemplify, I read in a not to far past Biophysical >Journal, that, even with simplified, shortened sequences (<20aa) it was >difficult for some experts to make a computer fold alpha-helices by >strict algorithms. Even these weren't all that close to emperical >observation. > How big is your protein, and what is it's name? If you can find an >ancestor close enough (>50% homology); mutate it, minimize the energy, >and send it through molecular dynamics, and you _might_ have a good >guess. > This can all be done with Tripos' SYBYL. Let us know how things work >out. > >Deacon Sweeney >Wright State University I would add only one caution to this recipe for a homology model - if there is one lesson which has come out of the protein structure prediction conferences, it is that "refinement" of modeled structures rarely if ever leads toward the correct structure. This includes minimization and dynamics. Their main effect seems to be to push the model in one of the many vectors which do not connect the model and the actual structure. Many of the most succesful modelers currently use strictly conservative methods with constrained minimization to relieve the most gross problems, while acknowledging that while this method is unlikely to yield the correct structure in every detail, it consistently gives the best approximation. Good luck. Mike *************************************************** * Michael J. Bower, Ph.D. * Computational Chemistry/Molecular Modeling Group * SmithKline Beecham Pharmaceuticals * 709 Swedeland Road * PO Box 1539 UW2430 * King of Prussia, PA 19406 * (610) 270-5907 fax: (610) 270-4490 * bowermj@mh.us.sbphrd.com * My views are my own. *************************************************** From owner-molec-model@net.bio.net Fri Feb 12 22:00:00 1999 Path: biosci!daresbury!not-for-mail From: jonnygn@hotmail.com Newsgroups: bionet.molec-model Subject: President Clinton is out of the office! Date: 13 Feb 1999 01:44:18 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 20 Message-ID: <7a2ldi$jio$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk content-length: 114 Return-Path: Apparently-To: The President is out of the Office! "http://www.presidentclinton.com" Check it out! From owner-molec-model@net.bio.net Sat Feb 13 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!dispose.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!not-for-mail From: amartin@stagleys.demon.co.uk (Andrew Martin) Newsgroups: bionet.molec-model Subject: Re: Proteins 3D Date: Sat, 13 Feb 1999 17:42:38 GMT Organization: Private Address Message-ID: References: X-Trace: mail2news.demon.co.uk 918965744 mail2news:4738 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!finch-post-10.mail.demon.net!post.mail.demon.net![194.222.20.72]!stagleys.demon.co.uk X-Newsreader: TIN [version 1.2 PL2] Lines: 17 Michael J. Bower (bowermj@mh.us.sbphrd.com) wrote: : I would add only one caution to this recipe for a homology model - if there : is one lesson which has come out of the protein structure prediction : conferences, it is that "refinement" of modeled structures rarely if ever : leads toward the correct structure. This includes minimization and dynamics. I'd agree with that. Only in rare cases is the RMSd reduced by minimisation and then only marginally. Look at my paper on the analysis of the CASP2 comparative modelling section (PROTEINS: Structure, Function and Genetics, Suppl 1 (1997), 14-28) Andrew From owner-molec-model@net.bio.net Sat Feb 13 22:00:00 1999 From: "The Flavored Coffee Guy" Subject: Microscope Design Concept which eliminates the need for staining cell tissues. Date: Sun, 14 Feb 1999 03:30:32 -0500 Lines: 81 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: <#G8AiO$V#GA.262@upnetnews03> Newsgroups: bionet.molec-model NNTP-Posting-Host: 1cust54.tnt5.orlando.fl.da.uu.net [208.251.132.54] Path: biosci!rutgers!uwm.edu!news-out.cwix.com!newsfeed.cwix.com!207.68.152.14!upnetnews04!upnetnews03 http://pc65.frontier.osrhe.edu/hs/science/emspec.gif Looking at the radio spectrum in order to define which compounds, and elements are present have frequently been used in astronomy. But, in the field of microscopy this form of information gathering isn't utilized. In this post are links that consist of the parts of highest significance required to build a microscope that doesn't require stains, or staining procedures to view cell tissues. A tunable laser is used as a light source in order to align the spectral lines generated in spectroscopy associated to a sample being viewed. Minimum amounts of light enable the reflectivity, or absorption lines found to either be reflected or absorbed within in a minimum number of atoms, or molecules. Therefore, the image multiplier tube is used to amplify what little light is used to unveil the internal, or external structures of the cell being examined. Basing the lasers output frequency to be an issue resolved by computer controls, stepping the laser through it's output frequency range. Retrieving a series of images produced on a one image, per step in frequency would enable software to retrieve, and compile an image based on the absorbed, or reflected wavelengths of light. Accumulating this information using software to generate a multiple of grayscale images which would be placed in the visible range of colors generated by a computer by spacing the gray images in a false color spectrum map, then letting the computer compress the scale into the visible range for viewing. Based on the objective of viewing the translucent cells, such as neural tissues, and doing so without damaging them. The light exiting the source is polarized in order to determine the polarize state of molecules which are being viewed. If this is included in the frequency/image stepping sequence, several images will need to be take based on the degree of rotation of the interference lenses rotation. This lens is a secondary rotatable polarized lens that is used for interference to detect the degree at which polarized light rotates passing through any given molecule. Further stepping modifications include detailing focal lengths, and calibrating a robotic drive assembly to generate a 3 dimensional model of a cell in a computer based on objective, and focal length. This would amount to either an auto focus system, or focusing on the highest point of a cell, and then the slide. From there the computer would asses the cell in steps in the first order. If the microscopes software follows through this full featured design sequence properly the order of events are as follows. 1. Objective start step, and finish step pinion settings. 2. Step 1 of the tunable laser frequency, either the highest, or lowest. 3. Polarized Rotation stepping and images are accumulated. 4. Next Objective step. 5. Goto step 3 until Objective step = last step. 6. Next laser output frequency. 7. Goto 3 until laser output frequency = last frequency. A binary search would be used to find the image files which contained the highest contrast, and mark, or rename each file. Then use the compressed light range to generate a complete image out of overlaying the images produced in the grayscale format. I have leave you with the three dimensional stuff, because that's a trigonometric function of boxes in a box. Selected tunable laser Diode sites http://www.maycomm.com/ http://aesd.larc.nasa.gov/C/CF/CF12f.html Robotics positioner assemblies. http://mwrn.com/product/light_microscopy/accessories.htm Instrument grade low light Imaging tube spec sheet. http://www.burle.com/cgi-bin/byteserver.pl/pdf/4804h.pdf The Flavored Coffee Guy. From owner-molec-model@net.bio.net Sun Feb 14 22:00:00 1999 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!unixg.ubc.ca!byron!sness From: sness@FIX.TIN.DOMAIN (Steven Ness) Newsgroups: bionet.molec-model Subject: Announcement - Free 3D Docking Visualization Date: 15 Feb 1999 19:49:21 GMT Organization: The University of British Columbia Lines: 15 Message-ID: <7a9to1$10d$1@nntp.ucs.ubc.ca> NNTP-Posting-Host: byron.biochem.ubc.ca X-Newsreader: TIN [version 1.2 PL2] I'd like to announce the first public release of DockCam, a small 3D visualization program to view docking results. It reads PDB files, and is well suited to reading in large numbers of molecules, for quick and easy visualization. It's totally FREE! Executables for SGI and Linux are available. To get it go to: www.dockvision.com Steven Ness. From owner-molec-model@net.bio.net Sun Feb 14 22:00:00 1999 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-east1.sprintlink.net!-program!news-peer1.sprintlink.net!news.sprintlink.net!news.maxwell.syr.edu!isdnet!wanadoo.fr!not-for-mail From: "Bootch-1" Newsgroups: alt.penthouse.sex.pictures,alt.penthouse.sex.wanted.models,alt.sex.girls,alt.sex.pictures.female,alt.sex.wanted.models,alt.supermodels,alt.supermodels.cindy-crawford,alt.supermodels.claudia-schiffer,aus.rail.models,bionet.molec-model,rec.nude Subject: !!! LAETICIA CASTA !!! Date: Tue, 16 Feb 1999 00:07:35 +0100 Organization: Wanadoo - (Client of French Internet Provider) Lines: 5 Message-ID: <7aa973$9ti$1@platane.wanadoo.fr> NNTP-Posting-Host: tntmetz10-254.abo.wanadoo.fr X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Come on ! If you like the famous Model Laeticia Casta, visit this : http://models.software-space.com/casta/ From owner-molec-model@net.bio.net Mon Feb 15 22:00:00 1999 From: bkfmvu@meramera.com Newsgroups: bionet.molec-model Subject: Learn The Secrets Of Classified Advertising 8499 [1/2] Lines: 10 Message-ID: <2B3y2.12047$lp5.1772@news.rdc1.tn.home.com> Date: Tue, 16 Feb 1999 01:11:26 GMT NNTP-Posting-Host: 24.4.113.194 X-Complaints-To: abuse@home.net X-Trace: news.rdc1.tn.home.com 919127486 24.4.113.194 (Mon, 15 Feb 1999 17:11:26 PDT) NNTP-Posting-Date: Mon, 15 Feb 1999 17:11:26 PDT Organization: @Home Network Path: biosci!news.ic.sunysb.edu!news-nysernet-16.sprintlink.net!news-east1.sprintlink.net!-program!news-peer1.sprintlink.net!news.sprintlink.net!nntp.abs.net!newshub2.home.com!newshub1.home.com!news.home.com!news.rdc1.tn.home.com.POSTED!not-for-mail Nationwide NewspapersTM is a professionally developed Windows® based program. It includes an electronic directory of over 4,000 Daily & Weekly newspapers. Other menu options include statewide advertising associations. This option can place your ad in 100’s of papers, with millions of readers, all with just one phone call. Many of these papers will cost you less than one dollar each! This powerful new program will also include Network and Group advertising associations. They can place your advertisement Locally, Regionally, or Nationally. You can select from a variety of publications including, daily, weekly, free weeklies, shoppers and more. We include pricing, deadlines and contact information. You can save a large amount of money and time using these "secret" advertising sources. http://www.firstchoicemkt.com/d2060.html Hope these site is helpful to promote your business. ijqurnndgqvhnuqjdtzdnnyldnuqmpgqw From owner-molec-model@net.bio.net Mon Feb 15 22:00:00 1999 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!news.algonet.se!newsfeed1.telenordia.se!algonet!isdnet!wanadoo.fr!not-for-mail From: "Bootch" Newsgroups: alt.supermodels,alt.supermodels.cindy-crawford,alt.supermodels.claudia-schiffer,aus.rail.models,bionet.molec-model,rec.nude Subject: FREE FREE FREE FREE FREE Date: Tue, 16 Feb 1999 23:26:25 +0100 Organization: Wanadoo - (Client of French Internet Provider) Lines: 4 Message-ID: <7acse6$qtr$2@platane.wanadoo.fr> NNTP-Posting-Host: tntmetz10-35.abo.wanadoo.fr X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 http://models.softcare-space.com/casta/ From owner-molec-model@net.bio.net Wed Feb 17 22:00:00 1999 Path: biosci!SLIP.NET!grizzly From: grizzly@SLIP.NET (Michael Sherrell) Newsgroups: bionet.molec-model Subject: ABI 377 for sale Date: 18 Feb 1999 15:56:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BE5B56.A4E46860@oak-hiper1a-41-105.dialup.slip.net> NNTP-Posting-Host: net.bio.net Newly for sale: ABI 377 DNA sequencer, XL, 96 lanes, under transferrable Perkin Elmer service contract until March 2000. Price: $105,000. I also have these peptide and oligo synthesizers and sequencers, LC-mass specs and NMRs for sale: Synthesizers and sequencers: ABI 394 synthesizer, valve blocks rebuilt, warranteed: $12,500          ABI Procise 492 protein sequencer, $59,000 ABI 3948 synthesizer: inquire ABI 390Z synthesizer, 50-100uM yields: $4,000        ABI 373 stretch, 5-filter, Genescan, under ABI service: $19,500 Li-Cor 4000LS, 1994 model: <$20,000 ABI 430, working: $6,000 ABI 430, rebuilt, warranteed: $10,500 ABI 433, upgraded by ABI from 431: $39,000 Advanced ChemTech 396 Multiple Biomolecule Synthesizer, unused: $45,000 PerSeptive 9050+, $6,000 + a variety of other ABI, PerSeptive, HP, Biosearch, ACT, etc. synthesizers and sequencers LC-MS: PE Sciex API III+, 5yrs old, ES, APCI (installation available): $82,000 Finnigan TSQ 7000, installed, warranty: $149,000      Finnigan TSQ 700, 1995; NOT Y2K compliant; under Finnigan service now: $80,000 HP 5989B, extended mass range (2000 amu), hex ion guide (HPLC, installation & warranty available): $45,000 NMRs: Bruker AMX-500, installed: $175,000 Bruker AC-250, running in lab now: $30,000 Varian Gemini 300: $70,000 . Please contact me to discuss any of these, or if you have any items you might like to sell. Michael Sherrell Grizzly Analytical 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com From owner-molec-model@net.bio.net Wed Feb 17 22:00:00 1999 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.gtei.net!wn3feed!worldnet.att.net!135.173.83.225!attworldnet!newsadm From: carter.john@worldnet.att.net (John Mark Carter) Newsgroups: alt.drugs.chemistry,alt.advanced.placed.or.honors.chemistry.2,alt.sci.physics,bionet.molec-model,ntu.sci.chemistry Subject: Re: Anyone know some good compound databases? Date: 18 Feb 1999 13:22:20 GMT Organization: AT&T WorldNet Services Lines: 22 Message-ID: <36cc0f44.1993221@netnews.worldnet.att.net> References: <7agjmt$h3k$1@oak.prod.itd.earthlink.net> NNTP-Posting-Host: 12.78.103.123 X-Newsreader: Forte Free Agent 1.1/32.230 On Thu, 18 Feb 1999 00:30:13 -0800, "user793871" wrote: >I am looking for some databsaes on the net that have information about >speciific compounds. Hopefully a model of tehm as well. Anyone know of >something? >I know of one called the CIS (Chemical Information System) but I cant find >it on the net. >Please email me. >Sincerely >user793871@earthlink.net > > > Check info.CAS.org or www.chemcenter.org From owner-molec-model@net.bio.net Wed Feb 17 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!lsanca1-snf1!news.gtei.net!newsfeed1.earthlink.net!nntp.earthlink.net!posted-from-earthlink!not-for-mail From: "user793871" Newsgroups: alt.drugs.chemistry,alt.advanced.placed.or.honors.chemistry.2,alt.sci.physics,bionet.molec-model,ntu.sci.chemistry Subject: Anyone know some good compound databases? Date: Thu, 18 Feb 1999 00:30:13 -0800 X-ELN-Insert-Date: Thu Feb 18 00:45:05 1999 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 Organization: EarthLink Network, Inc. X-Posted-Path-Was: not-for-mail Lines: 10 NNTP-Posting-Host: 1cust163.tnt3.long-beach.ca.da.uu.net X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-ELN-Date: 18 Feb 1999 08:41:01 GMT Message-ID: <7agjmt$h3k$1@oak.prod.itd.earthlink.net> I am looking for some databsaes on the net that have information about speciific compounds. Hopefully a model of tehm as well. Anyone know of something? I know of one called the CIS (Chemical Information System) but I cant find it on the net. Please email me. Sincerely user793871@earthlink.net From owner-molec-model@net.bio.net Thu Feb 18 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.gtei.net!news.new-york.net!uunet!ffx.uu.net!in3.uu.net!news2.i-2000.com!ebrown From: ebrown@i-2000.com (Ellie Brown) Newsgroups: bionet.molec-model Subject: post doc position protein modeling Date: Thu, 18 Feb 1999 21:19:28 -0500 Organization: home Lines: 2 Message-ID: NNTP-Posting-Host: dyn88.access4.nyc.i-2000.net X-Newsreader: MT-NewsWatcher 2.4.4 Check this URL for details. http://www.ars.usda.gov/afm/hrd/hrdhomepage/vacancy/9912H.HTM From owner-molec-model@net.bio.net Fri Feb 19 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.berkeley.edu!newsfeed1.earthlink.net!nntp.earthlink.net!posted-from-earthlink!not-for-mail From: "Borgwiser" Newsgroups: alt.drugs.chemistry,alt.advanced.placed.or.honors.chemistry.2,alt.sci.physics,bionet.molec-model,ntu.sci.chemistry Subject: Re: Anyone know some good compound databases? Date: Fri, 19 Feb 1999 21:31:12 -0500 References: <7agjmt$h3k$1@oak.prod.itd.earthlink.net> X-Posted-Path-Was: not-for-mail X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-ELN-Date: 20 Feb 1999 02:33:21 GMT X-ELN-Insert-Date: Fri Feb 19 18:35:11 1999 Organization: EarthLink Network, Inc. X-Newsreader: Microsoft Outlook Express 4.72.3110.1 Lines: 4 NNTP-Posting-Host: sdn-ar-002gaatlap187.dialsprint.net Message-ID: <7al6th$s2m$1@fir.prod.itd.earthlink.net> http://webbook.nist.gov From owner-molec-model@net.bio.net Sat Feb 20 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsswitch.lcs.mit.edu!newsfeed.cwix.com!207.114.4.11!nntp.abs.net!newshub2.home.com!news.home.com!news.rdc1.bc.wave.home.com.POSTED!not-for-mail From: "Achim Recktenwald" Newsgroups: alt.drugs.chemistry,alt.advanced.placed.or.honors.chemistry.2,alt.sci.physics,bionet.molec-model,ntu.sci.chemistry References: <7agjmt$h3k$1@oak.prod.itd.earthlink.net> Subject: Re: Anyone know some good compound databases? Lines: 22 X-Newsreader: Microsoft Outlook Express 4.72.3155.0 X-Mimeole: Produced By Microsoft MimeOLE V4.72.3155.0 Message-ID: Date: Sun, 21 Feb 1999 00:44:58 GMT NNTP-Posting-Host: 24.64.220.105 X-Complaints-To: abuse@home.net X-Trace: news.rdc1.bc.wave.home.com 919557898 24.64.220.105 (Sat, 20 Feb 1999 16:44:58 PDT) NNTP-Posting-Date: Sat, 20 Feb 1999 16:44:58 PDT Organization: @Home Network Canada Try http://www.chemfinder.com/ The search-engine gives not only basic data to the compound of interest - the chemical structure, as well - and then a long list of cross-references in other web-databases - extremely helpful. Achim user793871 wrote in message <7agjmt$h3k$1@oak.prod.itd.earthlink.net>... >I am looking for some databsaes on the net that have information about >speciific compounds. Hopefully a model of tehm as well. Anyone know of >something? >I know of one called the CIS (Chemical Information System) but I cant find >it on the net. >Please email me. >Sincerely >user793871@earthlink.net > > > From owner-molec-model@net.bio.net Sun Feb 21 22:00:00 1999 Path: biosci!AOL.COM!NONIE619 From: NONIE619@AOL.COM Newsgroups: bionet.molec-model Subject: ATTN: Account holder Date: 22 Feb 1999 03:01:13 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Internet User: To start let me say this, I'm tired of the porn email in my email box and all that click here crap. I'm a published author in the United States, Germany and Japan. I've spend seven hours or more a day for the last two months researching the topic of Spam on the Internet. I've learned a lot about SMTP blocking, reporting Spam, and blocking your email account from being spammed. In this time I have practiced everything I have learned in blocking this crap mail they call professional advertising and in the last few weeks I have not yet received one piece of Spam. I wrote a full report on this process I have developed and did some research on how to get this information around to the right people. I've contacted many spammers and did some price research, what better way to find the Spam haters then to find the spammer that is spamming them. I've talked to many well known bulkers as they like to be called and we made the agreement that I will get to advertise to there list in return for a profit break. I'm forced to sell my report for the reason to pay the advertising fee and keep me alive but on the bright side you will learn to fight against the horrible porn mail in your email box. Please join me in fighting this horrible advertising method that has been on the Internet for years. Remember, "Together we stand, divided we fall." To order my detailed report and provide your help in fighting spam send $15 to the address below and lets all, together, put a stop to spam once and for all. K.C. Smith 10 East Louisiana Evansville, IN 47711 Thank you for your support in this matter. Your friend and best man in fight against spam. From owner-molec-model@net.bio.net Sun Feb 21 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: NONIE619@aol.com Newsgroups: bionet.molec-model Subject: ATTN: Account holder Date: 22 Feb 1999 15:12:31 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 40 Message-ID: <7ars4v$66r$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk content-length: 1695 Return-Path: Apparently-To: Dear Internet User: To start let me say this, I'm tired of the porn email in my email box and all that click here crap. I'm a published author in the United States, Germany and Japan. I've spend seven hours or more a day for the last two months researching the topic of Spam on the Internet. I've learned a lot about SMTP blocking, reporting Spam, and blocking your email account from being spammed. In this time I have practiced everything I have learned in blocking this crap mail they call professional advertising and in the last few weeks I have not yet received one piece of Spam. I wrote a full report on this process I have developed and did some research on how to get this information around to the right people. I've contacted many spammers and did some price research, what better way to find the Spam haters then to find the spammer that is spamming them. I've talked to many well known bulkers as they like to be called and we made the agreement that I will get to advertise to there list in return for a profit break. I'm forced to sell my report for the reason to pay the advertising fee and keep me alive but on the bright side you will learn to fight against the horrible porn mail in your email box. Please join me in fighting this horrible advertising method that has been on the Internet for years. Remember, "Together we stand, divided we fall." To order my detailed report and provide your help in fighting spam send $15 to the address below and lets all, together, put a stop to spam once and for all. K.C. Smith 10 East Louisiana Evansville, IN 47711 Thank you for your support in this matter. Your friend and best man in fight against spam. From owner-molec-model@net.bio.net Tue Feb 23 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!remarQ73!supernews.com!remarQ.com!remarQ69!not-for-mail From: Guillermo Moyna Newsgroups: bionet.molec-model Subject: Gaussian 98 stuff Date: Wed, 24 Feb 1999 08:18:37 -0600 Organization: Texas A&M University Lines: 15 Message-ID: <36D40A3D.4615@cbnmr.chem.tamu.edu> Reply-To: gmoyna@cbnmr.chem.tamu.edu NNTP-Posting-Host: 208.244.157.46 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: 919862202 /KEVRR7EI9D2ED0F4C usenet52.supernews.com X-Complaints-To: newsabuse@remarQ.com X-Mailer: Mozilla 3.03Gold (Win95; I) Dear netters, Does anybody knows a trick to make Gaussian98 calculate chemical shifts at the MP2 level? Supposedly it should do it, but I'm having big problmes. Please, answer me by e-mail... -- Guillermo Moyna, PhD Department of Chemistry and Biochemistry University of the Sciences in Philadelphia 600 South 43rd Street, PA 19104-4495 Phone: (215)-596-8552 (ext. 1) e-mail: g.moyna@usip.edu From owner-molec-model@net.bio.net Tue Feb 23 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsswitch.lcs.mit.edu!newsfeed.cwix.com!192.232.20.2!malgudi.oar.net!hyperion.wright.edu!news.wright.edu!not-for-mail From: deacon Newsgroups: bionet.molec-model Subject: class libraries Date: Wed, 24 Feb 1999 10:27:44 -0500 Organization: Wright State University Lines: 5 Message-ID: <36D41A70.588B@wright.edu> Reply-To: sweeney.2@wright.edu NNTP-Posting-Host: lx012pc84775.wright.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) I am looking for C++ class libraries relevant to molecular dynamics. Does anyone know where I might find some? Deacon Sweeney Wright State University From owner-molec-model@net.bio.net Wed Feb 24 22:00:00 1999 From: spg@jabez.anu.edu.au (Steve Greatbanks) Newsgroups: bionet.molec-model Subject: Re: Gaussian 98 stuff References: <36D40A3D.4615@cbnmr.chem.tamu.edu> Message-ID: X-Newsreader: slrn (0.9.4.6 UNIX) NNTP-Posting-Host: 150.203.193.248 X-NNTP-Posting-Host: 150.203.193.248 Date: 25 Feb 1999 10:57:54 +1000 X-Trace: 25 Feb 1999 10:57:54 +1000, 150.203.193.248 Organization: Australian National University Path: biosci!news.stanford.edu!logbridge.uoregon.edu!woodstock.news.demon.net!demon!news.maxwell.syr.edu!intgwpad.nntp.telstra.net!news1.optus.net.au!optus!clarion.carno.net.au!spg Lines: 72 In article <36D40A3D.4615@cbnmr.chem.tamu.edu>, Guillermo Moyna wrote: >Dear netters, > >Does anybody knows a trick to make Gaussian98 calculate chemical shifts >at the MP2 level? Supposedly it should do it, but I'm having big >problmes. Please, answer me by e-mail... Guillermo, You should expect people to reply to newsgroups if you send a question in a newsgroup - could be useful to people other than you. I've followed up as well sending you an email copy (as a courtesy). Anyway, I'm not sure what your problem exactly is because you fail to describe it, but test415 of the gaussian test suite appears to be what you are looking for... (I do not know if you have the programmer's reference or the source for g98). This works on all our machines here --start-- #p mp2/6-311G(df,pd) 5d 7f Units=Bohr NMR test First section of Gaussian Test Job 415: Fluoro-ethylene MP2 NMR 0,1 F -2.02476070 0.33315211 .00000000 C 0.24111266 -0.85292320 .00000000 C 2.40542436 0.41348845 .00000000 H 0.04195708 -2.89204527 .00000000 H 2.44295852 2.45832509 .00000000 H 4.17176525 -0.61421962 .00000000 --end-- As you can see, the only non-standard bit in here is the 5d 7f part. However, these are not the source of the problem... For some reason, options like #p mp2/3-21g nmr=giao do not set the right route and do not enter l1002, but the exactly equivalent command line of #p mp2/3-21g nmr Works fine! In summary, just ensure that if you are using nmr=giao (which seems to be the best method anyway), make sure you just use the equivalent `nmr'. If you need to use the other nmr methods, set them using iop(10/45=xx) where xx=1 for single gauge origin, xx=2 for IGAIM and xx=4 for CSGT. The route generator appears to be rather ill i.e. #p mp2/3-21g nmr works (checked) #p mp2/3-21g nmr=giao is broken (checked) Hope that helps, Steve Greatbanks ps - this is with g98a6 -- +---------------------------------------+--+--------------------------------+ | Dr Stephen P. Greatbanks | | | | Biochemistry & Molecular Biology |w:| http://biocomp.anu.edu.au/~spg | | John Curtin School of Medical Research|e:| Steve.Greatbanks@anu.edu.au | | Australian National University |p:| (+61) (02) 6279 8305 (JCSMR) | | ACT 0200, Australia | | | +---------------------------------------+--+--------------------------------+ From owner-molec-model@net.bio.net Wed Feb 24 22:00:00 1999 Path: biosci!NETSGO.COM!airhead From: airhead@NETSGO.COM ("=?euc-kr?B?x+PDorW1?=") Newsgroups: bionet.molec-model Subject: www.biostudy.net/Q&A Date: 24 Feb 1999 18:53:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <000701be6069$2fdb8220$874e73d2@1> Reply-To: "=?euc-kr?B?x+PDorW1?=" NNTP-Posting-Host: net.bio.net This is a multi-part message in MIME format. ------=_NextPart_000_0004_01BE60B4.9DB335E0 Content-Type: text/plain; charset="euc-kr" Content-Transfer-Encoding: base64 UGxlYXNlIHZpc2l0IGhlcmUgYW5kIGxpbmsgeW91ciBwZXJzb25hbCBvciBsYWIgc2l0ZQ0KdGhl biBkaXNjdXNzaW9uIHJhcGlkbHkgYW5kIGVhc2lseSAuDQogDQpodHRwOi8vd3d3LmJpb3N0dWR5 Lm5ldC9RJkENCg== ------=_NextPart_000_0004_01BE60B4.9DB335E0 Content-Type: text/html; charset="euc-kr" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBXMyBIVE1MLy9FTiI+DQo8SFRNTD4N CjxIRUFEPg0KDQo8TUVUQSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9a3NfY181NjAxLTE5 ODciIGh0dHAtZXF1aXY9Q29udGVudC1UeXBlPg0KPE1FVEEgY29udGVudD0nIk1TSFRNTCA0Ljcy LjMxMTAuNyInIG5hbWU9R0VORVJBVE9SPg0KPC9IRUFEPg0KPEJPRFkgYmdDb2xvcj0jZmZmZmZm Pg0KPERJVj4NCjxESVY+PEZPTlQgY29sb3I9IzAwMDAwMCBzaXplPTI+UGxlYXNlIHZpc2l0IGhl cmUgYW5kIGxpbmsgeW91ciBwZXJzb25hbCBvciBsYWIgDQpzaXRlPC9GT05UPjwvRElWPg0KPERJ Vj48Rk9OVCBjb2xvcj0jMDAwMDAwIHNpemU9Mj50aGVuIGRpc2N1c3Npb24gcmFwaWRseSBhbmQg ZWFzaWx5IA0KLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgY29sb3I9IzAwMDAwMCBzaXplPTI+ PC9GT05UPiZuYnNwOzwvRElWPg0KPERJVj48Rk9OVCBjb2xvcj0jMDAwMDAwIHNpemU9Mj48QSAN CmhyZWY9Imh0dHA6Ly93d3cuYmlvc3R1ZHkubmV0L1EmQSI+aHR0cDovL3d3dy5iaW9zdHVkeS5u ZXQvUSZhbXA7QTwvQT48L0ZPTlQ+PC9ESVY+PC9ESVY+PC9CT0RZPjwvSFRNTD4NCg== ------=_NextPart_000_0004_01BE60B4.9DB335E0-- From owner-molec-model@net.bio.net Thu Feb 25 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news-lond.gip.net!news.gsl.net!gip.net!newspeer.clara.net!news.clara.net!news5.cableinet.net!cableinet-uk!news1.cableinet.co.uk!not-for-mail From: "Andrew M Smith" Newsgroups: bionet.microbiology,bionet.molbio.news,bionet.molbio.proteins,bionet.molec-model,bionet.neuroscience Subject: Announcement: Independent Equipment Appraisals Date: Fri, 26 Feb 1999 18:30:52 -0000 Organization: selectscience Lines: 36 Message-ID: <7b6q7f$ndr$3@news1.cableinet.co.uk> NNTP-Posting-Host: ppp-1-10-52.access.telinco.net X-Trace: news1.cableinet.co.uk 920054831 23995 212.1.138.116 (26 Feb 1999 18:47:11 GMT) X-Complaints-To: abuse@cableinet.net NNTP-Posting-Date: 26 Feb 1999 18:47:11 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: biosci bionet.microbiology:15938 bionet.molbio.proteins:14021 bionet.molec-model:2425 bionet.neuroscience:28081 Dear Fellow Scientist, Through your career, you have surely worked with many different pieces of equipment. Some of these will have been very reliable, well-designed and particularly appropriate for your application. Some of them, though, will have been less reliable, or not particularly suitable for your specific application. When considering a laboratory purchase, word-of-mouth recommendations amongst immediate colleagues regarding the suitability of a piece of equipment has always been a reliable guide. Imagine being able to share valuable appraisals with scientists all over the world, from every manufacturer, for every application! Now an independent team of professionals (with over 20 years' experience in publishing the highest-quality information on scientific equipment and techniques) has developed the next-generation solution to this problem. SelectScience (http://www.selectscience.net) is a powerful WWW-site that allows scientists all over the world to share their opinions on every piece of laboratory equipment, from every manufacturer, for every type of application. The opinions of real scientists, of "real world" usage of laboratory equipment and instrumentation will be found on the site (http://www.selectscience.net), and scientists in your position will come to the site to help with their planned equipment purchases. In order to get SelectScience off to a flying start, we would like to invite you to become an early contributor to the site. If you feel you have a constructive comment to make about your experiences with one or more products (either positive or negative), please register with the SelectScience site (www.selectscience.net), find the appropriate products, and add your opinions to our database. You will be helping your fellow laboratory scientists around the world, and might even win yourself a personalized T-shirt, a palmtop computer or even a digital camera. The laboratory community needs your help - we are waiting for your visit! Andrew Smith Editor, www.selectscience.net From owner-molec-model@net.bio.net Fri Feb 26 22:00:00 1999 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Feb 1999 02:00:13 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199902271000.CAA06267@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. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. 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 Sat Feb 27 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!remarQ-uK!remarQ.com!supernews.com!diablo.theplanet.net!news.theplanet.net!newspost.theplanet.net!not-for-mail From: "Don Ainley" Newsgroups: alt.drugs.chemistry,alt.advanced.placed.or.honors.chemistry.2,alt.sci.physics,bionet.molec-model,ntu.sci.chemistry Subject: Re: Anyone know some good compound databases? Date: Sun, 28 Feb 1999 20:19:37 -0000 Organization: Customer of Planet Online Lines: 5 Message-ID: <7bc8n1$g03$1@news6.svr.pol.co.uk> References: <7agjmt$h3k$1@oak.prod.itd.earthlink.net> NNTP-Posting-Host: modem-5.cobalt.dialup.pol.co.uk X-Trace: news6.svr.pol.co.uk 920233505 16387 62.136.13.5 (28 Feb 1999 20:25:05 GMT) NNTP-Posting-Date: 28 Feb 1999 20:25:05 GMT X-Complaints-To: abuse@theplanet.net X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Try http://webbook.nist.gov/chemistry/ for organic compounds. Don Ainley From owner-molec-model@net.bio.net Sun Feb 28 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!diablo.theplanet.net!news.theplanet.net!newspost.theplanet.net!not-for-mail From: "Don Ainley" Newsgroups: alt.drugs.chemistry,alt.advanced.placed.or.honors.chemistry.2,alt.sci.physics,bionet.molec-model,ntu.sci.chemistry Subject: Re: Anyone know some good compound databases? Date: Mon, 1 Mar 1999 14:07:52 -0000 Organization: Customer of Planet Online Lines: 8 Message-ID: <7be7a7$j7p$1@news6.svr.pol.co.uk> References: <7agjmt$h3k$1@oak.prod.itd.earthlink.net> NNTP-Posting-Host: modem-9.vanadium.dialup.pol.co.uk X-Trace: news6.svr.pol.co.uk 920297607 19705 62.136.11.9 (1 Mar 1999 14:13:27 GMT) NNTP-Posting-Date: 1 Mar 1999 14:13:27 GMT X-Complaints-To: abuse@theplanet.net X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Try webbook.nist.gov/chemistry/ for organic compounds. Don Ainley From owner-molec-model@net.bio.net Sun Feb 28 22:00:00 1999 Path: biosci!CORNELL.EDU!eev1 From: eev1@CORNELL.EDU (Elaine Van Etten) Newsgroups: bionet.molec-model Subject: Faculty Position Available Date: 1 Mar 1999 11:45:37 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 82 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net PalatinoMOLECULAR BIODIVERSITY OF PLANTS The Boyce Thompson Institute for Plant Research at Cornell University invites applications for a tenure-track position for a junior level scientist who uses genomics or proteomics approaches to study fundamental mechanisms underlying plant biodiversity at the organismal or population levels. Research areas of interest include, but are not limited to: - Adaptation to biotic or abiotic stresses or environmental factors - Genetics and biochemistry of plant-insect or plant-pathogen interactions - Molecular analysis of ecological systems The successful candidate will establish an independent, extramurally-funded research program and collaborate with colleagues at the Boyce Thompson Institute and elsewhere on the Cornell University campus. This position is synergistic with the Cornell Genomics Initiative which is a comprehensive effort to recruit 20 new genomics faculty to the Cornell campus and significantly upgrade facilities and infrastructure for genomics and proteomics research. Excellent start-up funds and benefits are available. Review of applications will begin April 5, 1999 and continue until the position is filled. Applicants should send a curriculum vitae, statement of research interests, and names of at least three references to Molecular Biodiversity Search Committee, Boyce Thompson Institute, Ithaca, New York 14853. Questions regarding the position may be directed to Dr. David Stern, 607-254-1306; e-mail ds28@cornell.edu or Dr. Robert Kohut, 607-254-1233, e-mail rjk9@cornell.edu. Boyce Thompson Institute is a private, independent, non-profit research institute formally affiliated with Cornell University. The institute is an affirmative action, equal opportunity employer and is committed to increasing the diversity of its faculty and staff. Applications from women and minorities are encouraged.