From owner-molec-model@net.bio.net Thu Jul 01 06:38:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!ihug.co.nz!not-for-mail From: "Marcel Dinger" Newsgroups: bionet.molec-model Subject: Genamics - Software, Journals, Genomes Date: Thu, 1 Jul 1999 19:27:11 +1200 Organization: Genamics Lines: 33 Message-ID: <930814381.368@ham.ihug.co.nz> Reply-To: "Marcel Dinger" NNTP-Posting-Host: ham.ihug.co.nz X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Cache-Post-Path: ham.ihug.co.nz!unknown@p89-max7.ham.ihug.co.nz X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) Genamics Molecular Biology and Modeling Resources at http://genamics.com just got better: With over 650 software entries, 360 journal speed links, and 100+ genome project links, you can be assured that you can find what you need, and find it quickly. 1. SoftwareSeek - The largest collection of software tools available for Windows, MS-DOS, Unix, Linux and Macintosh platforms. Entries are classifed into several categories, including DNA sequence analysis, protein structure analysis, RNA structure prediction, molecular modeling, image analysis, and sequence alignment. 2. GenomeSeek - A searchable database of current information about microbial genome projects with links to relevant sites and publications. The database contains over 100 entries. 3. JournalSeek - A searchable index to hundreds of journals, providing easy access to a wealth of information. JournalSeek presently contains more than 360 journals, in a broad range of topics including molecular biology, biochemistry, microbiology, neuroscience, immunology, and cancer. We are committed to keeping the information on our pages as up-to-date as possible and encourage input from our users. We don't require any sort of log-in procedure, and our pages are not loaded with cumbersome advertising banners. Marcel Dinger, Genamics. From owner-molec-model@net.bio.net Thu Jul 01 14:13:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!isdnet!pasteur.fr!jussieu.fr!news!univ-lille1.fr!not-for-mail From: "Philippe CHAVATTE" Newsgroups: bionet.molec-model Subject: Proteins comparison Date: Thu, 1 Jul 1999 17:04:42 +0200 Organization: Universite des Sciences et Technologies de LILLE, France Lines: 20 Message-ID: <7lg082$vu6$1@netserv.univ-lille1.fr> NNTP-Posting-Host: icp16.univ-lille2.fr X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 What is the best methodology to compare two protein 3D structures (pdb format) ? What criteria permit to affirm their similarity ? Many thanks for your help. Philippe ----------------- Philippe CHAVATTE Institut de Chimie Pharmaceutique Albert Lespagnol BP 83 59006 LILLE CEDEX FRANCE E-Mail : pchavatt@phare.univ-lille2.fr From owner-molec-model@net.bio.net Fri Jul 02 06:25:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!dispose.news.demon.net!demon!colt.net!news-lond.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!jussieu.fr!moka.ccr.jussieu.fr!not-for-mail From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN) Newsgroups: bionet.molec-model Subject: Re: Proteins comparison Date: 2 Jul 1999 09:19:34 +0200 Organization: CCR - Universites Paris VI/VII - Paris - France Message-ID: <7lhp66$4t98@moka.ccr.jussieu.fr> NNTP-Posting-Host: moka.ccr.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: vishnu.jussieu.fr 930899932 27644 134.157.1.23 (2 Jul 1999 07:18:52 GMT) X-Complaints-To: Newsmaster@jussieu.fr@vishnu.jussieu.fr NNTP-Posting-Date: 2 Jul 1999 07:18:52 GMT Lines: 23 Subject: Re: Proteins comparison In article: <7lg082$vu6$1@netserv.univ-lille1.fr> "Philippe CHAVATTE" wrote: >What is the best methodology to compare two protein 3D structures (pdb >format) ? >What criteria permit to affirm their similarity ? >Many thanks for your help. > >Philippe I do not know which is the best, but I can email you CSR, which works for any pair of molecules, i.e. the atomic numbering is not important. The criterion is the number of atoms in the common 3D motif. Just specify for which platform (SGI, RS6000, CRAY, LINUX, DEC-alpha) and system version. Note that I take 3 weeks holidays from tomorrow, and that the freeware will be probably sent at the end of July. Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, ESA 7086) ptitjean@ccr.jussieu.fr From owner-molec-model@net.bio.net Fri Jul 02 06:34:00 1999 Path: biosci!SINICA.EDU.TW!shihds From: shihds@SINICA.EDU.TW ("Edward S.C. Shih") Newsgroups: bionet.molec-model Subject: Least Squares Fitting of two structures Date: 2 Jul 1999 00:34:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <377D4B79.DED324DB@sinica.edu.tw> NNTP-Posting-Host: net.bio.net Hi all, I am urgently looking for a program (or subroutin) and detail algorithm about least squares fitting of two protein structures. Please tell me where to find them. Thanks a lot. Edward S.C. Shih Institute of BioMedical Science, Academia Sinica, Taipei, Taiwan e-mail: shihds@gate.sinica.edu.tw From owner-molec-model@net.bio.net Fri Jul 02 07:35:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.enteract.com!cyclone.i1.net!uunet!ffx.uu.net!news1-gui.server.ntli.net!news5-gui.server.ntli.net!ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!biosci From: ljovine@nki.nl (Luca Jovine) Newsgroups: bionet.molec-model Subject: Re: Least Squares Fitting of two structures Date: 2 Jul 1999 09:29:15 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 25 Message-ID: References: <377D4B79.DED324DB@sinica.edu.tw> NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 930904156 24796 193.62.192.80 (2 Jul 1999 08:29:16 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 2 Jul 1999 08:29:16 GMT X-Received: from nki.nl (Hermes.nki.nl [192.42.114.8]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id JAA15784 for ; Fri, 2 Jul 1999 09:29:12 +0100 (BST) X-Received: from localhost by nki.nl (5.x/SMI-SVR4) id AA22998; Fri, 2 Jul 1999 10:32:11 +0200 X-To: "Edward S.C. Shih" X-Cc: molmodel@hgmp.mrc.ac.uk X-In-Reply-To: <377D4B79.DED324DB@sinica.edu.tw> > Hi all, > I am urgently looking for a program (or subroutin) and detail > algorithm about least squares fitting of two protein structures. Please > tell me where to find them. > Thanks a lot. Hi Edward, try ProFit from Andrew Martin! You can get it from: http://www.biochem.ucl.ac.uk/~martin/swreg.html Hope this helps, good luck - Luca. -------------------------------------------------------------------------------- Luca Jovine Protein Crystallography Group Voice: +31.(0)20.512-1959/1964/1969 The Netherlands Cancer Institute FAX: +31.(0)20.512-1954 Molecular Carcinogenesis Division E-mail: ljovine@nki.nl OR luca@nki.nl Plesmanlaan 121 1066 CX Amsterdam, The Netherlands -------------------------------------------------------------------------------- --- From owner-molec-model@net.bio.net Fri Jul 02 11:24:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newspeer.monmouth.com!tank.news.pipex.net!pipex!uunet!ams.uu.net!ffx.uu.net!news1-gui.server.ntli.net!news5-gui.server.ntli.net!ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!biosci From: TIY@phys.chem.msu.ru (Ivan Torshin) Newsgroups: bionet.molec-model Subject: [Fwd: [Fwd: Proteins comparison]] Date: 2 Jul 1999 13:18:15 +0100 Organization: MSU Chem dept Lines: 207 Message-ID: <377CAC12.6D70E44@phys.chem.msu.ru> NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------135440291BD025BEF3A875B6" X-Trace: niobium.hgmp.mrc.ac.uk 930917896 1521 193.62.192.80 (2 Jul 1999 12:18:16 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 2 Jul 1999 12:18:16 GMT X-Received: from beta.chem.msu.ru (beta.chem.msu.ru [195.208.208.11]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA02172 for ; Fri, 2 Jul 1999 13:18:09 +0100 (BST) X-Received: from phys.chem.msu.ru (phys315.chem.msu.ru [195.208.208.169]) by beta.chem.msu.ru (8.9.3/8.9.3) with ESMTP id QAA02670 for ; Fri, 2 Jul 1999 16:18:02 +0400 (MSD) X-Mailer: Mozilla 4.03 [en] (Win95; I) X-To: molmodel@hgmp.mrc.ac.uk This is a multi-part message in MIME format. --------------135440291BD025BEF3A875B6 Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hello, following are the answers to the question for pdb-l list. best regards, Ivan. Subject: Re: [Fwd: Proteins comparison] Date: Fri, 2 Jul 1999 09:34:26 +0100 (GMT Daylight Time) From: Geoff Barton To: Ivan Torshin CC: PDB-L list There are a number of different techniques around for comparing protein three dimensional structures. Some are available as WWW servers. This is certainly NOT a complete list so apologies to anyone I've left out, but you might try DALI at EBI (http://www2.ebi.ac.uk/dali), CATH at UCL (http://www.biochem.ucl.ac.uk/bsm/cath/server/index.html) and VAST at NCBI (http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html). Each has its own way of scoring similarity. Many programs are also downloadable so that you can run them on your own computer. One available from me is STAMP which is a suite of programs for pairwise and multiple structure alignment, database searching and general manipulation of protein coordinate files (see http://barton.ebi.ac.uk/ and click on 'software'). Hope this helps, Geoff. On Thu, 1 Jul 1999, oded wrote: > Ivan Torshin wrote: > > > Subject: Proteins comparison > > Date: Thu, 1 Jul 1999 17:04:42 +0200 > > From: "Philippe CHAVATTE" > > Organization: Universite des Sciences et Technologies de LILLE, France > > To: molmodel@hgmp.mrc.ac.uk > > > > What is the best methodology to compare two protein 3D structures (pdb > > format) ? > > What criteria permit to affirm their similarity ? > > Many thanks for your help. > > > > Philippe > > > > ----------------- > > > > Philippe CHAVATTE > > Institut de Chimie Pharmaceutique Albert Lespagnol > > BP 83 > > 59006 LILLE CEDEX > > FRANCE > > > > E-Mail : pchavatt@phare.univ-lille2.fr > > -- > ---------------------------------------------------------------- > " If we knew what it was we were doing, > it would not be called research, > would it?" > Albert Einstein (1879-1955) > ---------------------------------------------------------------- > Oded Livneh E-mail: > oded@compugen.co.il > Compugen Ltd. Tel: +972-3-765-8585 > > 72 Pinchas Rosen Street, Direct: +972-3-765-8529 > Tel-Aviv 69512, Israel Fax: +972-3-765-8555 > Web Site: > http://www.cgen.com > =================================== > > > > > *** Details on how to be removed from this list as well as an *** > *** archive of recent postings are available at *** > *** http://www.rcsb.org/pdb/forum.html *** > > ------------------ Dr Geoff. Barton, EMBL-European Bioinformatics Institute, Genome Campus, Hinxton, Cambs CB10 1SD, U.K., mailto:geoff@ebi.ac.uk http://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496 --------------135440291BD025BEF3A875B6 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline Received: by beta.chem.msu.ru (mbox b178) (with Cubic Circle's cucipop (v1.31 1998/05/13) Fri Jul 2 16:07:50 1999) X-From_: geoff@ebi.ac.uk Fri Jul 2 12:38:06 1999 Return-Path: Received: from alpha1.ebi.ac.uk (root@alpha1.ebi.ac.uk [193.62.196.122]) by beta.chem.msu.ru (8.9.3/8.9.3) with ESMTP id MAA00705 for ; Fri, 2 Jul 1999 12:37:57 +0400 (MSD) Received: from dhcp8.ebi.ac.uk (dhcp8.ebi.ac.uk [193.62.196.110]) by alpha1.ebi.ac.uk (8.8.7/8.8.7) with ESMTP id JAA08859; Fri, 2 Jul 1999 09:37:47 +0100 (BST) Date: Fri, 2 Jul 1999 09:34:26 +0100 (GMT Daylight Time) From: Geoff Barton To: Ivan Torshin cc: PDB-L list Subject: Re: [Fwd: Proteins comparison] In-Reply-To: <377BBA79.B02AA500@compugen.co.il> Message-ID: X-X-Sender: geoff@alpha1.ebi.ac.uk MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There are a number of different techniques around for comparing protein three dimensional structures. Some are available as WWW servers. This is certainly NOT a complete list so apologies to anyone I've left out, but you might try DALI at EBI (http://www2.ebi.ac.uk/dali), CATH at UCL (http://www.biochem.ucl.ac.uk/bsm/cath/server/index.html) and VAST at NCBI (http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html). Each has its own way of scoring similarity. Many programs are also downloadable so that you can run them on your own computer. One available from me is STAMP which is a suite of programs for pairwise and multiple structure alignment, database searching and general manipulation of protein coordinate files (see http://barton.ebi.ac.uk/ and click on 'software'). Hope this helps, Geoff. On Thu, 1 Jul 1999, oded wrote: > Ivan Torshin wrote: > > > Subject: Proteins comparison > > Date: Thu, 1 Jul 1999 17:04:42 +0200 > > From: "Philippe CHAVATTE" > > Organization: Universite des Sciences et Technologies de LILLE, France > > To: molmodel@hgmp.mrc.ac.uk > > > > What is the best methodology to compare two protein 3D structures (pdb > > format) ? > > What criteria permit to affirm their similarity ? > > Many thanks for your help. > > > > Philippe > > > > ----------------- > > > > Philippe CHAVATTE > > Institut de Chimie Pharmaceutique Albert Lespagnol > > BP 83 > > 59006 LILLE CEDEX > > FRANCE > > > > E-Mail : pchavatt@phare.univ-lille2.fr > > -- > ---------------------------------------------------------------- > " If we knew what it was we were doing, > it would not be called research, > would it?" > Albert Einstein (1879-1955) > ---------------------------------------------------------------- > Oded Livneh E-mail: > oded@compugen.co.il > Compugen Ltd. Tel: +972-3-765-8585 > > 72 Pinchas Rosen Street, Direct: +972-3-765-8529 > Tel-Aviv 69512, Israel Fax: +972-3-765-8555 > Web Site: > http://www.cgen.com > =================================== > > > > > *** Details on how to be removed from this list as well as an *** > *** archive of recent postings are available at *** > *** http://www.rcsb.org/pdb/forum.html *** > > ------------------ Dr Geoff. Barton, EMBL-European Bioinformatics Institute, Genome Campus, Hinxton, Cambs CB10 1SD, U.K., mailto:geoff@ebi.ac.uk http://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496 --------------135440291BD025BEF3A875B6-- --- From owner-molec-model@net.bio.net Mon Jul 05 13:38:00 1999 Path: biosci!kfunigraz.ac.at!andreas.kungl From: andreas.kungl@kfunigraz.ac.at (andreas kungl) Newsgroups: bionet.molec-model Subject: 3rd International Conference on Molecular Structural Biology: Last call for Posters Date: 5 Jul 1999 07:38:02 -0700 Organization: Karl-Franzens-Universitaet Graz Lines: 330 Sender: daemon@net.bio.net Distribution: world Message-ID: <3780C092.6E6EA88B@kfunigraz.ac.at> NNTP-Posting-Host: net.bio.net The Biochemistry Subgroup of the Austrian Chemical Society is pleased to announce the Third International Conference on Molecular Structural Biology ICMSB99 which will take place in Vienna, Austria from September 8-12, 1999 FOR DETAILED INFORMATION, PLEASE SEE BELOW OR VISIT OUR HOMEPAGE AT http://www.kfunigraz.ac.at/ipcwww/icmsb99 ************************************************************************ Introduction to the ICMSB99 The First and the Second International Conference on Molecular Structural Biology (ICMSB) took place in Vienna in September 1995 and 1997. Both conferences were very well received by all who took part, including over 250 participants from more than 20 countries worldwide. The organisers are pleased to announce the Third ICMSB, which will take place from 8th to 12th September 1999, and which will, like the previous conferences, feature internationally renowned speakers. The ICMSB99 will focus on topics covering a number of the most exciting areas in the field, with the aim of bringing together specialised scientists from different areas. It will be opened by one of the most outstanding scientists in the field of structural biology, Robert Huber, and the following four days of sessions will include Folding and Function, Novel Structures, Advances in Microscopic Methods, Structural Molecular Biology, Structure-Based Drug Design, and Prediction and Simulation. ************************************************************************ Vienna - An Attractive Conference Location The ICMSB99 will be located at the Federal Chancellery in Vienna. The city is a particularly attractive location for a conference, with its combination of historical buildings, green parks, and modern architecture. Some of the most famous city sights include Schönbrunn Palace and the Hofburg, former homes of the Habsburgs, St. Stephans Cathedral, and the colourful Hundertwasser House. Also unique to Vienna is the Prater park, with its endless green avenues and its funfair, featuring the ´´Riesenrad´´ (ferris wheel). Of course, no trip to Vienna would be complete without a visit to one of the many traditional Viennese cafés, for a piece of the famous Sachertorte. An ´´Oldtimer-Tram´´tour around the Ringstraße will take participants past many of the finest sights. ************************************************************************ Organising Committee A. Kungl, P. Andrew, A. Binder, S. Kristl, A. Schilk ************************************************************************ Scientific Committee C. Kratky, M. Sippl, A. Kungl, P. Andrew ************************************************************************ In Cooperation With Austrian Academy of Sciences Austrian Federal Chancellery Austrian Federal Ministry of Science and Research ************************************************************************ Sponsored By Austrian Airlines Novartis Forschungsinstitut ************************************************************************ Scientific Programme The six sessions of the conference cover a wide range of topics and experimental methods, which will be presented in the form of plenary lectures, selected short oral communications, and posters. Wednesday 8th: Registration from 2 p.m. onwards Evening: Honorary Lecture (followed by a welcome drink and snack) Robert Huber (Max-Planck-Institute, Martinsried): Diversity and Conservation in Proteolytic Enzymes and their Inhibitors Thursday 9th: Morning Session: Advances in Microscopic Methods Werner Kühlbrandt (Max-Planck-Institute, Frankfurt): Two Conformations of Membrane Ion Pumps Hansgeorg Schindler (Linz University): Single Molecule Microscopy Methods for Structural Biology Helen Hansma (University of California, Santa Barbara): Probing Biomaterials with the Atomic Force Microscope Afternoon Session: Folding and Function Alan Fersht (Cambridge University): Minichaperones: Practical and Mechanistic Tools Thomas Kiefhaber (Biozentrum Basel): Speed Limit for Protein Folding Peter Wright (Scripps Institute): Structure and Dynamics of Unfolded Proteins and Protein Folding Intermediates Friday 10th: Morning Session: Novel Structures Michael Rossmann (Purdue University): The Assembly of Viruses Examined by Combining Crystallography and Cryo-electron Microscopy Don Wiley (Harvard University): Structural Studies of Viral Entry Mechanisms in Influenza, HIV-1 and bola Viruses Kurt Wüthrich (ETH Zürich): TROSY and BSE - Recent Progress with NMR in Structural Biology Afternoon Session: Structure-Based Drug Design Siegfried Reich (Agouron Pharmaceuticals): The Use of Protein Structural Information in Drug Design and Development: Some Examples Keith Wilson (Vertex Pharmaceuticals): Structure-Based Drug Design: Reality over Hype Poster Session I Saturday 11th: Morning Session: Structural Molecular Biology Stephen Cusack (EMBL Grenoble): tRNA and Amino Acid Recognition by Aminoacyl-tRNA Synthetases Robert Kaptein (Utrecht University): Allosteric Interactions in Protein-DNA Recognition Christoph Kratky (Graz University): Structure and Mechanism of Enzymes with a B12 Cofactor Paul Sigler (Yale University): Structure and Function in Chaperonin-Assisted Protein Folding Afternoon: Poster Session II (followed by the ´´Oldtimer-Tram´´ tour) Sunday 12th: Morning Session: Structural Genomics David Eisenberg (UCLA): Protein-Protein Interactions Terry Gaasterland (Rockefeller University): Using Patterns of Evolution Across Whole Genomes to Support Structural Genomics Target Selection John Moult (University of Maryland): The Past, Present, and Future of Protein Structure Prediction Wayne Hendrickson (Columbia University): Prospects of High-Throughput Crystallographic Structure Determination Approx. 1 p.m.: End of Conference with Farewell Drink and Snack ************************************************************************ Call for Posters Interested participants are invited to submit abstracts describing original work which has not been presented elsewhere. Abstracts should arrive no later than July 10th, 1999. Authors will be informed about the provisional acceptance of the abstract by the end of July. The presentation of the abstract as a poster will be confirmed, and included in the Book of Abstracts when one or more of the authors registers for the conference. Contributors of outstanding abstracts will be chosen by the Scientific Committee to give a 15 minute oral presentation. Poster Prize A prize of ATS 2,000 will be awarded for the best poster contribution in terms of innovative results and presentation. ************************************************************************ Abstract Submission Camera-ready abstracts should be printed in good quality on a single (A4) sheet of paper, within the area 16 cm wide and 24 cm long. The title should be followed by the author(s) name(s), affiliation(s), and address(es). Text should be in a 12 point font with maximum 1.5 line spacing. Please send two unfolded copies of the abstract to the conference secretariat. ************************************************************************ Posters The poster boards will be 100 cm (width) x 200 cm (height). Materials for poster mounting will be provided. ************************************************************************ Conference Proceedings The lectures and poster presentations will be published by the Austrian Chemical Society in book form (with an ISBN number), and will be distributed to the participants upon arrival at the conference. Additional copies of the Conference Proceedings can be purchased for ATS 300,-. ************************************************************************ General Information Exhibition: An exhibition of instruments, accessories, software, literature, and other items is planned. Companies interested in displaying their products are kindly requested to contact the conference secretariat. Social Events: The conference will be opened by a welcome drink following the honorary lecture in the Federal Chancellery on the evening of Wednesday, September 8th. On Saturday afternoon, the conference participants will be taken on a tram tour of the city centre. Following this, all participants are encouraged to visit a typical Viennese Heurigen (wine cellar) to enjoy the local food and wine (not included in the registration fee). A further social event will be arranged for one other evening, leaving one evening free to explore Vienna. In addition, half day tours to some of Vienna´s best known sights will be organised for accompanying people (dependent on participant number). Registration (please contact the Conference Secretariat or our homepage): Registration Fee Before August 1 After August 1 Regular Participant 5.000 ATS 5.500 ATS GÖCH Member* 4.000 ATS 4.500 ATS Student** 2.500 ATS 3.000 ATS GÖCH-Students*/** 1.750 ATS 2.000 ATS Accompanying Person 500 ATS 600 ATS *Payment must be accompanied by proof of the remittance of the ´99-GÖCH membership fee **Payment must be accompanied by proof of student status The registration desk will be open from 2 p.m. on Wednesday, September 8th. The registration fee includes the Conference Proceedings and participation in all scientific sessions, the welcome and farewell drinks, lunch from Thursday to Saturday, coffee breaks, and participation in the social programme (please note: the Heurigen visit is not included). Accompanying people attend only the social programme (welcome drink, tram tour, additional evening). Accomodation is not included in the registration fee! For accomodation, to register for the Heurigen evening, and to book social events for accompanying people, please ask for the flyer of the travel agency MONDIAL CONGRESS (at the conference secretariat or at our homepage). Remittance of Fees: Remittance must be made in Austrian Schillings (ATS) payable to the Gesellschaft Österreichischer Chemiker, Arbeitsgruppe Biochemie, Account Number 0043-19265/04 at Bank Creditanstalt, Bank Code 11000. Payment is also accepted by sending a (Euro-)Cheque to the conference secretariat or by filling in the credit card form (Visa, Euro/Mastercard, Diners Club, and American Express are accepted). All charges due to bank transfer have to be paid by the sender. The sender´s name and address have to be clearly marked on every remittance. Cancellation: Applications may be cancelled up to August 1st, in which case 85% refund of fees already paid will be made. It will not be possible to offer any refunds if cancellations are made after that date. ************************************************************************ Conference Homepage Please visit our homepage at http://www.kfunigraz.ac.at/ipcwww/icmsb99 for the latest update of the programme plus further information. ************************************************************************ Key Dates July 10, deadline for submitting poster abstracts August 1, deadline for early registration fee August 1, deadline for cancellation ************************************************************************ Location Austrian Federal Chancellery (Bundeskanzleramt) Festsaal Radetzkystraße 2 A-1031 Vienna ************************************************************************ Conference Secretariat Dr. Andreas Kungl Austrian Chemical Society (GÖCH), Biochemistry Subgroupc/o Institute of Pharmaceutical Chemistry University of Graz, Universitätsplatz 1, A-8010 Graz Tel.: +43 316 380 5373, Fax: +43 316 382541 E-Mail: andreas.kungl@kfunigraz.ac.at From owner-molec-model@net.bio.net Mon Jul 05 21:14:00 1999 Path: biosci!news.stanford.edu!newsfeed.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 comparison Date: Mon, 05 Jul 1999 12:34:13 -0400 Organization: Wright State University Lines: 40 Message-ID: <3780DE85.41C6@wright.edu> References: <7lg082$vu6$1@netserv.univ-lille1.fr> NNTP-Posting-Host: linus.bmb.wright.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) There are numerous ways to compare 3D structures. Consider alpha-carbon rms differences upon superimposition. Consider sequence similarity based on many different kinds of criteria (identity, size, chemical similarity, average burial, etc). If you are trying to classify a protein's family, consider the latter. If you are modelling, consider the former, as well as the similarity between core residues (assuming you are working with a globular protein). Also use motif searches to guess at functional similarity. For a quick guess as to whether or not they are structurally analogous, perform a secondary structure alignment, much like a pairwise sequence alignment, looking for >70% identity (use internet resources for secondary structure determination, then align by hand). Again, it's somewhat difficult to answer without knowing what you are trying to accomplish. Thanks for your question. Deacon Sweeney Undergraduate phenomenon Wright State University Dayton, OH Philippe CHAVATTE wrote: > > What is the best methodology to compare two protein 3D structures (pdb > format) ? > What criteria permit to affirm their similarity ? > Many thanks for your help. > > Philippe > > ----------------- > > Philippe CHAVATTE > Institut de Chimie Pharmaceutique Albert Lespagnol > BP 83 > 59006 LILLE CEDEX > FRANCE > > E-Mail : pchavatt@phare.univ-lille2.fr From owner-molec-model@net.bio.net Wed Jul 07 01:52:00 1999 Path: biosci!PRISMA.IT!guy49 From: guy49@PRISMA.IT Newsgroups: bionet.molec-model Subject: Cable TV information .......IMPORTANT FYI Date: 6 Jul 1999 19:52:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 78 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907061674LAA15016@totalcoolness.ssy.co.kr> NNTP-Posting-Host: net.bio.net ENHANCE Your Cable TV! EASY to assemble plans for only $12.00 ! 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All orders WITHOUT a SELF ADDRESSED STAMPED ENVELOPE may be DELAYED. /\ /\ /\ sma From owner-molec-model@net.bio.net Fri Jul 09 09:30:00 1999 Path: biosci!CNET.CO.KR!tobaiwo52 From: tobaiwo52@CNET.CO.KR (pyrt8te) Newsgroups: bionet.molec-model Subject: Grandma's and businessman's new Internet tool. Date: 9 Jul 1999 03:30:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907094252XAA26153@ymutoas.u-3mrs.fr> NNTP-Posting-Host: net.bio.net Headline: With the iPhone even your Grandmother can surf and send email instantly-but wait until you see how it speeds up your business. Copy: Now your grandmother can get wired, your wife can divorce the desktop, your 6-yr. old can email your mom and you can increase your efficiency. The iPhone (as seen in PCWORLD, Red Herring, Baltimore Sun News) comes plug and play with a 56k modem, zero boot-up time, retractable laptop-size keyboard, 7.4 inch tiltable touchscreen, built-in digital answering machine and 2 lines. (Use the phone while sending email or surfing.) Did we say plug and play? Just $399. The king (pc) is dead. Long live the king (iPhone). For info on how to buy or sell call 603-537-0751, fax 603-537-0753, mail: iphone4u@bigfoot.com ADVD58E27-Exgh58S49 Mailz-Complyant V3. From owner-molec-model@net.bio.net Sun Jul 11 01:34:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!howland.erols.net!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: holson1000@aol.com (Howard Olson) Newsgroups: bionet.molec-model Subject: New Brookhaven PDB URL ? Lines: 3 NNTP-Posting-Host: ladder07.news.aol.com X-Admin: news@aol.com Date: 11 Jul 1999 02:28:27 GMT Organization: AOL http://www.aol.com Message-ID: <19990710222827.16895.00011341@ng-fw1.aol.com> What is the new URL for the Brookhaven Protein Data Bank? Howard From owner-molec-model@net.bio.net Sun Jul 11 09:08:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news-in-west1.sprintlink.net!news.sprintlink.net!news1-gui.server.ntli.net!news5-gui.server.ntli.net!ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!biosci From: mh270@mole.bio.cam.ac.uk (Miriam Hirshberg) Newsgroups: bionet.molec-model Subject: PDB URL Date: 11 Jul 1999 11:02:03 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 15 Message-ID: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 931687324 5994 193.62.192.80 (11 Jul 1999 10:02:04 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 11 Jul 1999 10:02:04 GMT X-Received: from mole.bio.cam.ac.uk (exim@mole.bio.cam.ac.uk [131.111.36.9]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA10777 for ; Sun, 11 Jul 1999 11:02:01 +0100 (BST) X-Received: from mh270 by mole.bio.cam.ac.uk with local (Exim 1.92 #3) id 113GQm-0006BA-00; Sun, 11 Jul 1999 11:01:56 +0100 X-To: molmodel@hgmp.mrc.ac.uk, holson1000@aol.com X-Reply-To: m.hirshberg@mole.bio.cam.ac.uk www2.ebi.ac.uk/pdb ====================================================================== Miriam (Miri) Hirshberg e-mail: m.hirshberg@mole.bio.cam.ac.uk Department of Biochemistry Tel : (+44) 01223 766018 University of Cambridge Tel : (+44) 01223 333600 (switch board) 80 Tennis Court Road Fax : (+44) 01223 766002 Old Addenbrooke's Site Cambridge CB2 1GA, UK ===================================================================== --- From owner-molec-model@net.bio.net Mon Jul 12 02:11:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!outgoing.news.rcn.net.MISMATCH!feed1.news.rcn.net!rcn!newsfeed.gol.com!wnoc-tyo-news!news.nc.u-tokyo.ac.jp!gray.ims.u-tokyo.ac.jp!not-for-mail From: RECOMB 2000 Newsgroups: bionet.molec-model Subject: RECOMB 2000 Date: Mon, 12 Jul 1999 12:00:56 +0900 Organization: Human Genome Center, Inst. of Medical Science, Univ. of Tokyo, Japan. Lines: 211 Message-ID: <37895A68.9CF57C88@ims.u-tokyo.ac.jp> NNTP-Posting-Host: pine.ims.u-tokyo.ac.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.6 [ja] (Win95; I) X-Accept-Language: ja FIRST CALL FOR PAPERS FOURTH ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 2000) April 8-11, 2000 Tokyo, Japan Organized by Human Genome Center, Institute of Medical Science, University of Tokyo Sponsored by ACM (Association for Computing Machinery) - SIGACT with support from Compugen IBM Corporation International Society for Computational Biology SLOAN Foundation SmithKline Beecham US National Science Foundation US Department of Energy http://recomb2000.ims.u-tokyo.ac.jp The Fourth Annual Conference on Research in Computational Molecular Biology (RECOMB 2000), sponsored by the Association for Computing Machinery Special Interest Group on Algorithms and Computation Theory (ACM-SIGACT) with support from the SLOAN Foundation, US Department of Energy, US National Science Foundation, SmithKline Beecham, IBM Corporation, Compugen and ISCB will be organized by HGC, Institute of Medical Science, University of Tokyo, in Tokyo, Japan on April 8-11, 2000. The conference will be held at the Tokyo Big Sight International Exhibition Center. Papers reporting on original research (both theoretical and experimental) in all areas of computational molecular biology are sought, including surveys of important recent results/directions. Typical but not exclusive topics of interest include: - Genomics, - Molecular sequence analysis, - Recognition of genes and regulatory elements, - Molecular evolution, - Protein structure, - Gene Expression, - Gene Networks, - Combinatorial libraries and drug design, - Computational proteomics, - Functional genomics. ABSTRACT SUBMISSION: Authors are encouraged to submit their abstracts ELECTRONICALLY. Electronic submission instructions can be found at http://sigact.csci.unt.edu/~recomb2k/RECOMB2000.html. Authors who are unable to do so are requested to send 10 copies (preferably two sided copies) to: Prof. Ron Shamir RECOMB 2000 Program Chair Department of Computer Science Tel Aviv University Tel Aviv, 69978 Israel shamir@math.tau.ac.il An abstract must be received by September 30 1999, 23:59 EST. This is a firm deadline. Simultaneous submission to another conference or journal is allowed. Authors should inform the program chair at the time of submission of the simultaneous submission. CONFERENCE PROCEEDINGS: The extended abstracts for the Conference will be published by ACM Press and will be available at the Conference. A selection of the accepted extended abstracts in their final journal versions will be invited to appear in a special issue of the Journal of Computational Biology devoted to RECOMB 2000. NOTIFICATION: The conference submissions will be refereed by the program committee. Authors will be notified of acceptance or rejection by a letter mailed on or before December 5, 1999. A final copy of each accepted paper is required by January 5, 2000. An author of each accepted paper is expected to attend the Symposium and present the paper; otherwise alternative arrangements should be made to have the paper presented. ABSTRACT PREPARATION: An abstract should start with a succinct statement of the problem, the results achieved, their significance and a comparison with previous work. This material should be understandable to non-specialists. A technical exposition directed to the specialist should follow. The length, excluding cover page and bibliography, should not exceed 10 pages. The manuscript should be easy to read, using at least 11 point font size on U.S. standard 8 1/2 by 11 inch paper with no less than one inch margin all around. If authors believe that more details are absolutely necessary to substantiate the claims of the paper, they may include a clearly marked appendix. An E-mail address for the contact author should be included. Abstracts that deviate significantly from these guidelines risk rejection without consideration of their merits. POSTERS: RECOMB 2000 will include a poster session. Accepted posters will appear in a special poster book published by the Human Genome Center, University of Tokyo. Poster submission instructions will be announced later. CONFERENCE EVENTS: RECOMB 2000 will feature 9 Plenary Lectures (to be announced later) including the following conference events: - The Stanislaw Ulam Memorial Computational Biology Address: awarded by RECOMB to a scientist who has made major contributions in the computational aspects of the field. - The Distinguished Biology Lecture: awarded by RECOMB to a scientist who has made major contributions in the biological aspects of the field. - The Distinguished New Technologies Lecture: describing emerging, new technologies. - Best Paper by a Young Scientist Award: This award will be given to the best paper written solely by one or more recent graduates or students. An abstract is eligible if all authors are recent graduates (within 3 years from Ph.D.) or full-time students at the time of submission. This should be indicated in a letter to the program chair that accompanies the submission. The program committee may decline to make the award or may split it among several papers. CALENDAR Deadline for submission of papers: September 30th, 1999 Notification of acceptance/rejection: December 5th, 1999 Deadline for reception of final papers: January 5th, 2000 STEERING COMMITTEE Sorin Istrail, RECOMB General Vice-Chair Sandia National Laboratories, USA Richard Karp University of California, Berkeley, USA Thomas Lengauer GMD-SCAI, Germany Pavel Pevzner, RECOMB General Chair University of Southern California, USA Ron Shamir Tel-Aviv University, Israel Michael Waterman, RECOMB General Chair University of Southern California, USA PROGRAM COMMITTEE Steve Bryant NCBI, USA Andrea Califano IBM, USA Gordon Crippen University of Michigan, Ann Arbor, USA Ken Dill University of California San Francisco Richard Durbin Sanger Centre, UK Jim Fickett SmithKline Beecham, USA Phil Green University of Washington, Seattle, USA Dan Gusfield University of California, Davis, USA Sorin Istrail Sandia National Laboratories, USA Richard Karp University of California, Berkeley, USA Jonathan King MIT, USA George Komatsoulis Human Genome Sciences, USA Thomas Lengauer GMD-SCAI, Germany Michael Levitt Stanford University, USA Satoru Miyano University of Tokyo, Japan Pavel Pevzner University of Southern California, USA Gesine Reinert King's College, Cambridge, UK David Sankoff University of Montreal, Canada Ron Shamir, Program Committee Chair Tel-Aviv University, Israel Donna Slonim Whitehead Institute, USA Temple Smith Boston University, USA Mike Steel University of Canterbury, New Zealand Martin Vingron DKFZ, Heidelberg, Germany Lusheng Wang City University of Hong Kong, China Michael Waterman University of Southern California, USA Erik Winfree Princeton University, USA Haim Wolfson Tel Aviv University, Israel ORGANIZING COMMITTEE: Tatsuya Akutsu, Publicity Chair HGC, University of Tokyo, Japan Nir Friedman Hebrew University, Israel Osamu Maruyama HGC, University of Tokyo, Japan Satoru Miyano, Organizing Committee Chair HGC, University of Tokyo, Japan Kenta Nakai HGC, University of Tokyo, Japan Asako Suzuki, Registration Chair HGC, University of Tokyo, Japan Ayako Tomiyasu HGC, University of Tokyo, Japan Toshihisa Takagi, Treasurer HGC, University of Tokyo, Japan INFORMATION Human Genome Center Institute of Medical Science University of Tokyo 4-6-1 Shirokanedai, Minato-ku Tokyo 108-8639, Japan Phone: +81-3-5449-5615 Fax: +81-3-5449-5442 email : recomb2000@ims.u-tokyo.ac.jp http://recomb2000.ims.u-tokyo.ac.jp From owner-molec-model@net.bio.net Mon Jul 12 11:58:00 1999 Path: biosci!OSS1.LIV.AC.UK!kuagaa37 From: kuagaa37@OSS1.LIV.AC.UK (doc4diet) Newsgroups: bionet.molec-model Subject: ..Free Weight..Loss..Gift Date: 12 Jul 1999 05:58:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907121295GAA19910@spriouseq.upm.edu.my> NNTP-Posting-Host: net.bio.net Greetings from Roy Hinman II M.D., I am a Family Practice physician and Weight Loss Specialist. 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Date: 13 Jul 1999 03:41:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 123 Sender: daemon@net.bio.net Distribution: world Message-ID: <209.193102.798378@mailer2.cajunemail.com> NNTP-Posting-Host: net.bio.net We are a clearing house for targeted email lists, general lists and for advertising ! We have lists of every geographic market in the US. We have attorneys, investors (over 600,000), stockbrokers, insurance executives, high net-worth individuals, CEO's, marketing executives, sales-people, business associations, accountants, opportunity seekers, farmers, government workers, dentists, veterinarians, entertainment, golfers, gamblers, sports enthusiasts, fitness & health freaks, body-builders, just women, women's organizations, parents, , many many more... We have large numbers of domain lists like AT&T, AOL, COMPUSERVE, EARTHLINK, MCI, Sprintmail and many free services like Rocketmail, Hotmail, Juno, and many, many more. 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Ordering Just Call US @ (800) 242-0363 EXT. 2427 Opt in Option: Get on Our Opt in List, and receive only one email a day from Us and Receive access to free programs and many other goodies for remaining on the list for 90 days ! Receive a listing of many freebie sites including one that gives You 15,000 free items like free t-shirts, caps, free film and 14,997 other nifty items absolutely free of charge. From owner-molec-model@net.bio.net Tue Jul 13 09:42:00 1999 Path: biosci!bangor.ac.uk!m.a.hughes From: m.a.hughes@bangor.ac.uk ("M.A.Hughes") Newsgroups: bionet.molec-model Subject: Conformational analysis: explicit versus implicit solvation Date: 13 Jul 1999 03:42:49 -0700 Organization: University of Wales - Bangor Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <378B16BF.79AB@bangor.ac.uk> NNTP-Posting-Host: net.bio.net Hello, Does anyone have any experience of modelling small (2-6 residue) peptides using random conformational analysis procedures? I have modelled several tripeptides using the Sybyl package and their Random Search procedure (1000-5000 search iterations) with a distance-based dielectric constant of 80 to simulate water. I have now submitted a dipeptide to a similar conformational search except that I have included explicit waters (using the SILVERWARE algorithm and default settings) and a constant dielectric function of 80 to simulate bulk water outside of this solvation box. Specifically, I am interested in knowing two things: 1. How much longer will this sort of search take (it's been running nearly a week now!)? 2. Are the conformers found likely to be very different from those that would have been found using the simpler approximation to water of a distance-based dielectric function? Since I am interested in modelling a number of tri- to hexapeptides, the trade-off between computational time and "reliabilty/accuracy" of results is paramount. Thanks very much for any help, Neil ------------------------------------------------------------------------------ Neil J. Marshall Memorial Building Tel: +44 (01248) 351151 Ext. 2367 School of Biological Sciences Fax: +44 (01248) 370731 University of Wales, Bangor E-mail: bss219@bangor.ac.uk Gwynedd, LL57 2UW United Kingdom ------------------------------------------------------------------------------ From owner-molec-model@net.bio.net Tue Jul 13 14:55:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newshub.sdsu.edu!not-for-mail From: Neill White Newsgroups: bionet.molec-model Subject: Biomer : MM/MD on the web Date: Tue, 13 Jul 1999 15:57:31 +0000 Organization: The Scripps Research Institute Lines: 25 Message-ID: <378B61EB.857F4E93@scripps.edu> NNTP-Posting-Host: harpo-p31.sdsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Server-Date: 13 Jul 1999 15:49:01 GMT X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i586) X-Accept-Language: en Dear Colleagues, This is an announcement of the availability of a new molecular modeling program - Biomer - that is accessible over the web. It should be useful as an educational tool as well as a means to generate structures quickly and easily. It is written in Java, and version 1.0a has the following features: Model Builders for: nucleic acids (DNA/RNA) polypeptides polysaccharides Interactive molecule editor with fragment libraries Implementation of the AMBER force field Geometry Optimization with steepest descent / conjugate gradient Simulated Annealing with molecular dynamics Reads / Writes PDB files Exports jpeg, gif, and ppm images It is located at http://www.scripps.edu/~nwhite/Biomer/index.html Regards, Neill White From owner-molec-model@net.bio.net Tue Jul 13 23:38:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!novia!news-out.uswest.net!news.uswest.net!not-for-mail Message-ID: <378BDA1A.CA30BFC1@bioreason.com> From: Andrew Dalke Organization: Bioreason, Inc. X-Mailer: Mozilla 4.05C-SGI [en] (X11; U; IRIX64 6.5 IP30) MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: Re: PDB URL References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 11 Date: Tue, 13 Jul 1999 18:30:18 -0600 NNTP-Posting-Host: 207.108.245.3 X-Trace: news.uswest.net 931912350 207.108.245.3 (Tue, 13 Jul 1999 19:32:30 CDT) NNTP-Posting-Date: Tue, 13 Jul 1999 19:32:30 CDT holson1000@aol.com (Howard Olson): > What is the new URL for the Brookhaven Protein Data Bank? Miriam Hirshberg : > www2.ebi.ac.uk/pdb Actually, that's a mirror. The main site is: http://www.rcsb.org/pdb/ Andrew Dalke dalke@bioreason.com From owner-molec-model@net.bio.net Wed Jul 14 10:37:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!dispose.news.demon.net!demon!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!biosci From: D.Guthrie@Queens-Belfast.AC.UK ("David J.S. Guthrie") Newsgroups: bionet.molec-model Subject: Re: Conformational analysis: explicit versus implicit solvation Date: 14 Jul 1999 12:30:59 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 931951860 27119 193.62.192.80 (14 Jul 1999 11:31:00 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 14 Jul 1999 11:31:00 GMT X-Received: from Mailhub1.qub.ac.uk (isaiah.qub.ac.uk [143.117.143.16]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id MAA13640 for ; Wed, 14 Jul 1999 12:30:56 +0100 (BST) X-Received: from fujin.qub.ac.uk by Mailhub1.qub.ac.uk with SMTP-QUB (XT-PP) with ESMTP; Wed, 14 Jul 1999 11:30:53 +0000 X-Received: from [143.117.47.75] (djsguthrie.bc.qub.ac.uk [143.117.47.75]) by fujin.qub.ac.uk (8.8.8+Sun/8.8.8) with SMTP id MAA29226; Wed, 14 Jul 1999 12:27:40 +0100 (BST) X-To: "M.A.Hughes" X-cc: molmodel@hgmp.mrc.ac.uk X-Priority: NORMAL X-Mailer: Simeon for Macintosh Version 4.0.8 X-Authentication: IMSP Lines: 84 On 13 Jul 1999 03:42:49 -0700 "M.A.Hughes" wrote: > Hello, > > Does anyone have any experience of modelling small (2-6 residue) > peptides using random conformational analysis procedures? I have > modelled several tripeptides using the Sybyl package and their Random > Search procedure (1000-5000 search iterations) with a distance-based > dielectric constant of 80 to simulate water. I have now submitted a > dipeptide to a similar conformational search except that I have included > explicit waters (using the SILVERWARE algorithm and default settings) > and a constant dielectric function of 80 to simulate bulk water outside > of this solvation box. Specifically, I am interested in knowing two > things: > > 1. How much longer will this sort of search take (it's been running > nearly a week now!)? > 2. Are the conformers found likely to be very different from those that > would have been found using the simpler approximation to water of a > distance-based dielectric function? Since I am interested in modelling > a number of tri- to hexapeptides, the trade-off between computational > time and "reliabilty/accuracy" of results is paramount. > > Thanks very much for any help, > > Neil > ------------------------------------------------------------------------------ > Neil J. Marshall > > Memorial Building Tel: +44 (01248) 351151 Ext. 2367 > School of Biological Sciences Fax: +44 (01248) 370731 > University of Wales, Bangor E-mail: bss219@bangor.ac.uk > Gwynedd, LL57 2UW > United Kingdom > ------------------------------------------------------------------------------ Hi, It's some time since I dabbled with SYBYL but I have the following comments. a) Absolute calculation time will depend on the hardware which you haven't mentioned. However energy calculations on an assembly of n atoms involve approx. n x n interactions. If solvation increases the number of atoms to say 2n, calculation time will therefore take about 4 times longer! b) Realistic modelling of the dielectric constant is not trivial. Certainly you should never use a distance based constant of 80!!! The distance based constant (n/r) tries to model the bulk value (80 for water) at large values of r while allowing for increased interactions between charges which are close together and not separated by bulk water. By setting n = 80 you are grossly underestimating electrostatic interactions (almost completely neglecting them). I admit the manuals do not give explicit guidance. I tried modelling a small peptide containing Asp and Lys using n = 1 and found the sidechains of these residues were glued together, which certainly wasn't reflected in the NMR data. I increased n until such "unreasonable" behaviour ceased to be observed and found n= 4 prevented the electrostatic term dominating the interactions. I think I have seen n = 4 and n = 8 used in literature. c) I'm not sure it is sensible to do a conformational search with explicit solvation, since a conformational search is designed to find low energy conformations based on intra-molecular interactions. Solvation could of course alter the relative energies of conformations found by the search. The usual outcome of a conformational search is a series of low energy conformations (or of clusters of related conformations). I think it would be much quicker (and just as valid) to do the search without explicit solvent and then solvate and minimise each of the low enenrgy conformations found, to obtain realistic energies for comparison. Regards David ---------------------- David J.S. Guthrie, The Queen's University of Belfast, Centre for Peptide and Protein Engineering, School of Biology & Biochemistry, 97 Lisburn Road, Belfast BT9 7BL, N. Ireland, U.K. Tel (0)1232 272043 Fax (0)1232 236505 e.mail d.guthrie@qub.ac.uk --- From owner-molec-model@net.bio.net Wed Jul 14 11:14:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!colt.net!newspeer.clara.net!news.clara.net!remarQ-uK!remarQ.com!supernews.com!tank.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!biosci From: TIY@phys.chem.msu.ru (Ivan Torshin) Newsgroups: bionet.molec-model Subject: Re: Conformational analysis: explicit versus implicit solvation Date: 14 Jul 1999 13:08:53 +0100 Organization: MSU Chem dept Message-ID: <378C7BB6.58D31A5A@phys.chem.msu.ru> References: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 931954134 27479 193.62.192.80 (14 Jul 1999 12:08:54 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 14 Jul 1999 12:08:54 GMT X-Received: from beta.chem.msu.ru (beta.chem.msu.ru [195.208.208.11]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA16113 for ; Wed, 14 Jul 1999 13:08:40 +0100 (BST) X-Received: from phys.chem.msu.ru (phys315.chem.msu.ru [195.208.208.169]) by beta.chem.msu.ru (8.9.3/8.9.3) with ESMTP id QAA28006 for ; Wed, 14 Jul 1999 16:08:30 +0400 (MSD) X-Mailer: Mozilla 4.03 [en] (Win95; I) X-To: molmodel@hgmp.mrc.ac.uk Lines: 65 Dear colleagues, the following abstract may be of some interest as for water solvent models. The paper deals with molecular dynamics, however. Best regards Ivan Torshin. UI - 89362454 AU - Brooks CL 3d AU - Karplus M TI - Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme. LA - Eng MH - Animal MH - Binding Sites MH - Kinetics MH - Models, Molecular MH - Muramidase/*metabolism MH - Proteins/*metabolism MH - Solvents/*metabolism MH - Support, U.S. Gov't, P.H.S. MH - Thermodynamics RN - EC 3.2.1.17 (Muramidase) RN - 0 (Solvents) PT - JOURNAL ARTICLE DA - 19891005 DP - 1989 Jul 5 IS - 0022-2836 TA - J Mol Biol PG - 159-81 SB - M SB - X CY - ENGLAND IP - 1 VI - 208 JC - J6V AA - Author EM - 198912 AB - The stochastic boundary molecular dynamics methodology is applied to the active site of the enzyme lysozyme. A comparison is made of in vacuo dynamics results from the stochastic boundary method and a full conventional molecular dynamics simulation of lysozyme. Excellent agreement between the two approaches is obtained. The influence of solvent on the residues in the active site region is explored and it is shown that both the structure and dynamics are affected. Of particular importance for the structure of the protein is the solvation of polar residues and the stabilization of like-charged ion pairs. The magnitude of the fluctuations is only slightly altered by the solvent; the overall increase in the root-mean-square fluctuations, relative to the vacuum run, is 11%. The solvent effect on dynamical properties is found not to be simply related to the solvent viscosity. Both the solvent exposure and dynamic aspects of protein-solvent interactions, including the relative time scales of the motions, are shown to play a role. The effects of the protein on solvent dynamics and structure are also observed to be significant. The solvent molecules around atoms in charged, polar and apolar side-chains show markedly different diffusion coefficients as well as exhibiting different solvation structures. One key example is the water around apolar groups, which is much less mobile than bulk water, or water solvating polar groups. AD - Department of Chemistry, Harvard University, Cambridge, MA 02138. PMID- 0002769750 CU - 1991 SO - J Mol Biol 1989 Jul 5;208(1):159-81 --- From owner-molec-model@net.bio.net Wed Jul 14 20:57:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!btnet-peer!btnet!mendelevium.btinternet.com!not-for-mail From: Geoff Barton Newsgroups: bionet.molec-model Subject: Re: PDB URL Date: Wed, 14 Jul 1999 22:46:38 +0100 Organization: EMBL-EBI Message-ID: <378D053E.70D50257@ebi.ac.uk> References: <378BDA1A.CA30BFC1@bioreason.com> Reply-To: geoff@ebi.ac.uk NNTP-Posting-Host: host62-172-61-17.btinternet.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en Lines: 27 Well, actually EBI is far more than a mirror. Please see http://msd.ebi.ac.uk for details. Geoff. Barton Andrew Dalke wrote: > > holson1000@aol.com (Howard Olson): > > What is the new URL for the Brookhaven Protein Data Bank? > > Miriam Hirshberg : > > www2.ebi.ac.uk/pdb > > Actually, that's a mirror. The main site is: > http://www.rcsb.org/pdb/ > > Andrew Dalke > dalke@bioreason.com -- ------------------ Dr Geoff. Barton, EMBL-European Bioinformatics Institute, Genome Campus, Hinxton, Cambs CB10 1SD, U.K., mailto:geoff@ebi.ac.uk http://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496 http://msd.ebi.ac.uk, EMBL-EBI Macromolecular Structure Database From owner-molec-model@net.bio.net Thu Jul 15 20:48:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-out.uswest.net!news.uswest.net!not-for-mail Message-ID: <378E551A.65EE4AC6@bioreason.com> From: Andrew Dalke Organization: Bioreason, Inc. X-Mailer: Mozilla 4.05C-SGI [en] (X11; U; IRIX64 6.5 IP30) MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: Re: PDB URL References: <378BDA1A.CA30BFC1@bioreason.com> <378D053E.70D50257@ebi.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 22 Date: Thu, 15 Jul 1999 15:39:38 -0600 NNTP-Posting-Host: 207.108.245.3 X-Trace: news.uswest.net 932074909 207.108.245.3 (Thu, 15 Jul 1999 16:41:49 CDT) NNTP-Posting-Date: Thu, 15 Jul 1999 16:41:49 CDT Geoff Barton > Well, actually EBI is far more than a mirror. Thanks also to Miriam Hirshberg for correcting me on that. When I saw http://www2.ebi.ac.uk/pdb/ the first time it look very much like the original RCSB web page (not the new one they have now) and I didn't take a close enough look to see the very obvious EBI specific links. Actually what I thought was that the PDB has what I believe NCBI has, where there is a defined way to put mirror site specific information into the main page. So I saw the EBI links but because of the "look&feel" didn't think it was anything else. This also means I haven't spent much time wandering about the EBI pages since otherwise I would have seen that the page layout www2.ebi.ac.uk/pdb/ is consistent with the rest of the site. :) Andrew dalke@bioreason.com From owner-molec-model@net.bio.net Thu Jul 15 20:54:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!novia!news-out.uswest.net!news.uswest.net!not-for-mail Message-ID: <378E568C.A752602E@bioreason.com> From: Andrew Dalke Organization: Bioreason, Inc. X-Mailer: Mozilla 4.05C-SGI [en] (X11; U; IRIX64 6.5 IP30) MIME-Version: 1.0 Newsgroups: bionet.molec-model Subject: Re: Conformational analysis: explicit versus implicit solvation References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 16 Date: Thu, 15 Jul 1999 15:45:48 -0600 NNTP-Posting-Host: 207.108.245.3 X-Trace: news.uswest.net 932075279 207.108.245.3 (Thu, 15 Jul 1999 16:47:59 CDT) NNTP-Posting-Date: Thu, 15 Jul 1999 16:47:59 CDT D.Guthrie@Queens-Belfast.AC.UK ("David J.S. Guthrie") said: > a) Absolute calculation time will depend on the hardware which > you haven't mentioned. However energy calculations on an assembly > of n atoms involve approx. n x n interactions. If solvation > increases the number of atoms to say 2n, calculation time will > therefore take about 4 times longer! Not really relevant to the original question, but just addressing this statement. The O(N**2) term you mention comes from the electrostatics calculation, and there are ways to compute that in O(N log(N)) and even O(N) time. See: http://www.ee.duke.edu/research/SciComp/Docs/Dpmta/dpmta.html Andrew Dalke dalke@acm.org From owner-molec-model@net.bio.net Sat Jul 17 10:02:00 1999 Path: biosci!AOL.COM!ee89626 From: ee89626@AOL.COM Newsgroups: bionet.molec-model Subject: Credit # 253-695-4257-225 Date: 17 Jul 1999 04:02:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 77 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907171101.UAA03531@ds1.sysken.or.jp> NNTP-Posting-Host: net.bio.net ******************************************************* This gift certificate list is opt-in only. We are linked to many web sites that offer free subscriptions to our gift certificate list. You will be removed from this list at any time by following the simple instructions that can be found at the end of this email. THIS IS NOT SPAM! 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From owner-molec-model@net.bio.net Mon Jul 19 16:26:00 1999 Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!wn4feed!worldnet.att.net!144.212.100.101!newsfeed.mathworks.com!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: kottenhahn@icdd.com Newsgroups: bionet.molec-model,bionet.xtallography,news.chem.labware,news.chem.organomet Subject: ICDD CRYSTALLOGRAPHY SCHOLARSHIP AWARDS Date: Mon, 19 Jul 1999 17:14:54 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 72 Message-ID: <7mvme1$1r9$1@nnrp1.deja.com> NNTP-Posting-Host: 198.139.133.142 X-Article-Creation-Date: Mon Jul 19 17:14:54 1999 GMT X-Http-User-Agent: Mozilla/4.02 [en] (Win95; U) X-Http-Proxy: 1.0 x32.deja.com:80 (Squid/1.1.22) for client 198.139.133.142 X-MyDeja-Info: XMYDJUIDkottenhahn Xref: biosci bionet.molec-model:2628 bionet.xtallography:4837 INTERNATIONAL CENTRE FOR DIFFRACTION DATA CRYSTALLOGRAPHY SCHOLARSHIP AWARDS The science of crystallography has played a key role in the development of X-ray diffraction, electron diffraction and neutron diffraction for the elucidation of the atomic structure of matter. Crystallography is an interdisciplinary branch of science taught in departments of physics, chemistry, geology, molecular biology, metallurgy and material science. To encourage promising graduate students to pursue crystallographically oriented research, the International Centre for Diffraction Data (ICDD) has established a Crystallography Scholarship Fund. While the Ewald Prize is awarded every three years to an internationally recognized crystallographer, little effort has been made by science departments to cultivate aspiring crystallographers. Convinced of the beneficial, scientific impact of the proposed scholarships for crystallographically oriented research, the ICDD has solicited funds from private and industrial sectors to support this program. The ICDD has awarded twenty-eight scholarships in the amount of $2,000 each since 1992. The year 2000 Scholarship Award has been increased to $2,250. Applications for the year 2000 awards must be received by ICDD no later than 29 October 1999. 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From owner-molec-model@net.bio.net Wed Jul 21 10:24:00 1999 Path: biosci!MAIL.CIC.TSINGHUA.EDU.CN!leroy_qiao From: leroy_qiao@MAIL.CIC.TSINGHUA.EDU.CN (Qiao Li-An) Newsgroups: bionet.molec-model Subject: Quick Download PDB Files Date: 21 Jul 1999 04:24:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <0806.990721@mail.cic.tsinghua.edu.cn> Reply-To: Qiao Li-An NNTP-Posting-Host: net.bio.net Hello All, We can use SRS method to download a few PDB files, just click the search results one by one. But when we want to download thousands of protein structure PDB files, the task seems tedious. Now I have a list of PDB Entry ID Code. How can I get these PDB files from www directly? Could I use ftp to get all of them? Best regards, Qiao Li-An ----------------------------------------------------------- - Qiao Li-An - - Department of Biological Sciences and Technology, - - Tsinghua University, P.R.China , 100084 - - - - Tel: (86) 10-62784766(Office) - - (86) 10-62785049(Office) - - (86) 10-62775313(Dormitory) - - E-mail: leroy_qiao@mail.cic.tsinghua.edu.cn (default) - - leroy_qiao@263.net - ----------------------------------------------------------- From owner-molec-model@net.bio.net Thu Jul 22 11:45:00 1999 Path: biosci!KRYTEN.IPAX.COM.AU!cefa56 From: cefa56@KRYTEN.IPAX.COM.AU (trcomeruj) Newsgroups: bionet.molec-model Subject: 9-milyon fresh.leads - use the internet for.less Date: 22 Jul 1999 05:45:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907223285DAA27574@iocfreao.vghks.gov.tw> NNTP-Posting-Host: net.bio.net Have you ever gotten catalogs in the mail? Why would they do this? 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"Quality before Quantity" For info, FAX : 786-549-5787 Include your: name, email, telephone# *-+*-+*-+*-+*-+*-+*-+ This is a one time mailing and you have been automatically removed. *-+*-+*-+*-+*-+*-+*-+ From owner-molec-model@net.bio.net Thu Jul 22 13:07:00 1999 Path: biosci!biosci!not-for-mail From: geoff@ebi.ac.uk (Geoff Barton) Newsgroups: bionet.molec-model,bionet.xtallography Subject: UPDATE: EMBL-EBI Macromolecular Structure Database and the PDB Date: 22 Jul 1999 07:07:52 -0700 Organization: EMBL-European Bioinformatics Institute Lines: 93 Sender: daemon@net.bio.net Distribution: world Message-ID: <7n4h99$r74$1@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molec-model:2631 bionet.xtallography:4839 UPDATE: EMBL-EBI Macromolecular Structure Database and the PDB http://msd.ebi.ac.uk 1. GLASGOW IUCr MEETING If you are at the Glasgow meeting, you are welcome to visit our stand (5-9 August) and to attend the information session starting at 12:00 on 11th August. 2. DEPOSITION OF NEW STRUCTURES TO PDB AT EBI You may deposit structures to the PDB using AutoDep at EBI ( http://autodep.ebi.ac.uk ). If you need help completing the forms, please email pdbhelp@ebi.ac.uk. We will normally reply quickly during 09:00-17:00 GMT working hours. A PDB ID code will be issued by email as soon as the AutoDep session is completed. WHO PROCESSES DEPOSITIONS MADE AT EBI? All depositions made at EBI since 15th June 1999 have been processed by EBI- MSD staff. Entries that have been reviewed by the authors and reached their release date are forwarded each Monday to the RCSB for general distribution through the ftp site on Wednesday. WHAT IS THE FUTURE OF AUTODEP AT EBI? EBI-MSD is developing a new system for the management of data on the three dimensional structure of macromolecules. The deposition interface to this system will be phased-in starting in the Autumn of 1999. A demonstration of the new deposition system will be made at the IUCr Glasgow conference. DEPOSITIONS IN THE USA You can deposit to the PDB at the RCSB using the ADIT system (http://pdb.rutgers.edu). RCSB are also supporting AutoDep for continuing submissions started at Brookhaven National Laboratory. Data submitted to the USA site are processed by the RCSB. DOES IT MAKE ANY DIFFERENCE WHERE I DEPOSIT MY DATA? No. EBI-MSD and RCSB work closely to maintain consistent data processing procedures. You should choose the deposition site that is most convenient for your time zone. 3. QUERYING THE PDB There are a very large number of services on the WWW that provide access to the PDB and data derived from it. In this section we only mention tools that are directly related to the EBI-MSD, the former PDB at BNL and the RCSB. 3DB BROWSER EBI-MSD are continuing to support querying of the PDB by the tools http://www2.ebi.ac.uk/pdb-bin/pdbmain and http://www2.ebi.ac.uk/pdb-bin/pdblite. However, we are not enhancing or developing them. NEW EBI-MSD TOOLS Extensive work at EBI on clean-up of the legacy PDB files has led to the development of the following services: PQS http://msd.ebi.ac.uk/Services/Quaternary/quaternary.html provides access to the probable quaternary structures of macromolecules. 3Dseq http://msd.ebi.ac.uk/Services/Sequence/sequence.html provides a direct mapping between the PDB and SWISS-PROT sequence database at the residue level. Residue differences are annotated. Unpublished References http://msd.ebi.ac.uk/Services/UnPubRef/unpubref.html provides links to references for structures listed as Unpublished. New search tools are under development by the EBI-MSD project and these will be announced as they become available. NEW RCSB SEARCH TOOLS The RCSB offer a range of search tools. Please see http://www.rcsb.org/pdb/searchlite.html for information. 4. PDB FTP SITE AT EBI The RCSB maintain the ftp site that contains PDB format data files. At EBI we provide a full mirror (ftp://ftp.ebi.ac.uk/pub/databases/pdb) of this site in the same form as it was maintained by the former PDB at BNL. We will shortly also support a new simplified RCSB ftp site structure. 5. FEEDBACK If you believe you have found a problem with a released PDB entry, or have any questions or suggestions about EBI-MSD services, then please let us know by email to: pdbhelp@ebi.ac.uk. ------------ Geoff Barton, EMBL-European Bioinformatics Institute, Genome Campus, Hinxton, Cambs CB10 1SD, U.K., mailto:geoff@ebi.ac.uk http://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496 http://msd.ebi.ac.uk, EMBL-EBI Macromolecular Structure Database From owner-molec-model@net.bio.net Fri Jul 23 16:18:00 1999 Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!hammer.uoregon.edu!newsfeed.axxsys.net!nntp.abs.net!remarQ-easT!supernews.com!remarQ.com!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!biosci From: ljovine@nki.nl (Luca Jovine) Newsgroups: bionet.molec-model Subject: Re: Least Squares Fitting of two structures Date: 23 Jul 1999 18:12:25 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 24 Message-ID: References: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 932749946 22884 193.62.192.80 (23 Jul 1999 17:12:26 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 23 Jul 1999 17:12:26 GMT X-Received: from nki.nl (Hermes.nki.nl [192.42.114.8]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id SAA17489 for ; Fri, 23 Jul 1999 18:12:23 +0100 (BST) X-Received: from localhost by nki.nl (5.x/SMI-SVR4) id AA16951; Fri, 23 Jul 1999 19:15:40 +0200 X-To: molmodel@hgmp.mrc.ac.uk X-In-Reply-To: Ciao Pilvia, due righe per dirti che alla fine ho scelto New York. che dire, ho una bella strizza, ma ZP e' troppo interessante per non pigliare al volo l'occasione... quindi e' tardi per a'dam, ma puoi sempre venire a NY... in ogni caso, credo che comincero' a gennaio, e dall'11 a quasi-fine agosto doveri di nuovo essere a cambridge, per organizzare la grande rientrata in italia di tutto cio' che ho lasciato li' (ed e' una quantita' non indifferente di junk!), quindi ci si vede presto di sicuro (o vai in vacanza in quel periodo?)... Un bacio Luca. -------------------------------------------------------------------------------- Luca Jovine Macromolecular Crystallography Group Voice: +31.(0)20.512-1959/1964/1969 The Netherlands Cancer Institute FAX: +31.(0)20.512-1954 Molecular Carcinogenesis Division E-mail: ljovine@nki.nl Plesmanlaan 121 1066 CX Amsterdam, The Netherlands -------------------------------------------------------------------------------- --- From owner-molec-model@net.bio.net Fri Jul 23 16:36:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!biosci From: ljovine@nki.nl (Luca Jovine) Newsgroups: bionet.molec-model Subject: Re: Least Squares Fitting of two structures Date: 23 Jul 1999 18:30:09 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 21 Message-ID: References: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 932751010 23041 193.62.192.80 (23 Jul 1999 17:30:10 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 23 Jul 1999 17:30:10 GMT X-Received: from nki.nl (Hermes.nki.nl [192.42.114.8]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id SAA18319 for ; Fri, 23 Jul 1999 18:30:07 +0100 (BST) X-Received: from localhost by nki.nl (5.x/SMI-SVR4) id AA17194; Fri, 23 Jul 1999 19:33:24 +0200 X-To: molmodel@hgmp.mrc.ac.uk X-In-Reply-To: On 23 Jul 1999, Luca Jovine wrote: > Ciao Pilvia, (...) Ooops! I am *VERY* sorry - obviously entered the wrong email address alias... Luca. -------------------------------------------------------------------------------- Luca Jovine Macromolecular Crystallography Group Voice: +31.(0)20.512-1959/1964/1969 The Netherlands Cancer Institute FAX: +31.(0)20.512-1954 Molecular Carcinogenesis Division E-mail: ljovine@nki.nl Plesmanlaan 121 1066 CX Amsterdam, The Netherlands -------------------------------------------------------------------------------- --- From owner-molec-model@net.bio.net Sun Jul 25 20:14:00 1999 Path: biosci!VOL.VNN.VN!chelp From: chelp@VOL.VNN.VN Newsgroups: bionet.molec-model Subject: Repair your credit Date: 25 Jul 1999 14:14:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907252113.OAA04691@net.bio.net> NNTP-Posting-Host: net.bio.net Are you tired of having bad credit but don't know what you can do about it? Having a good credit rating can help you get the house or car of your dreams. Afford to put yourself or a child through college or take that vacation you have been dreaming about. Check out the website below for information on how to improve your credit rating and get the credit you deserve. http://3626046468/ns/credit2/ (cut and copy or type directly into your browser) From owner-molec-model@net.bio.net Tue Jul 27 08:00:00 1999 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Jul 1999 02:00:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907270900.CAA03026@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 Thu Jul 29 11:56:00 1999 From: mwin024@postbox.auckland.ac.nz (Markus Winter) Newsgroups: bionet.molec-model Subject: test - please ignore Date: Fri, 30 Jul 1999 00:26:20 +1200 Organization: Molecular Medicine Lines: 1 Message-ID: NNTP-Posting-Host: s.gilmour3.mmm.auckland.ac.nz X-Trace: scream.auckland.ac.nz 933251140 7687 130.216.55.163 (29 Jul 1999 12:25:40 GMT) X-Complaints-To: news@auckland.ac.nz NNTP-Posting-Date: 29 Jul 1999 12:25:40 GMT Path: biosci!agate!newsfeed.berkeley.edu!news-stock.gip.net!news.gsl.net!gip.net!news.iprolink.co.nz!auckland.ac.nz!s.gilmour3.mmm.auckland.ac.nz!user test