From owner-molec-model@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!sgigate.sgi.com!uhog.mit.edu!rutgers!oitnews.harvard.edu!oitnews.harvard.edu!nagle From: nagle@yuri.harvard.edu (Robert J. Nagle) Newsgroups: bionet.molec-model Subject: CHARMM available on PC platforms Date: 02 May 1996 22:42:10 GMT Organization: Harvard Chemistry Department Lines: 44 Message-ID: NNTP-Posting-Host: yuri.harvard.edu The widely used molecular dynamics package, {CHARMM}, is now available for platforms running OS/2 Warp. This version includes support for all of the commonly used features of CHARMM 24 (except for the QM/MM interface). The OS/2 support is available in two different distributions - an executable only (with the necessary parameter files etc.) and a complete source tape. The former is available on a set of floppies or via FTP and requires about 5MB of disk space to install. The latter will be available either by FTP, cartridge tape or DAT. As usual, in order to obtain a copy of CHARMM, a {license agreement} must first be executed with the CHARMM Development Project at Harvard University. The cost for the executable is $220 At least 16MB of RAM are required to run CHARMM under OS/2 - we recommend 24MB or more. On 24MB systems we have succesfully simulated systems up to 14,000 atoms. Performance for molecular dynamics simulations on a 75 MHz Pentium (24 MB) compared with an HP 735 workstation is System #atoms time(PC)/time(HP) alawat 2940 3.85 barnase 10124 4.08 bpti 892 4.16 crambin 396 5.03 mbco 14026 3.94 4.21 More information can be obtained from {http://yuri.harvard.edu/charmm} or by emailing marci@tammy.harvard.edu -- ------------------------------------------------------------------------------- Robert J. Nagle nagle@tammy.harvard.edu Dept. of Chemistry, M/S 223, Harvard University (617) 495-0787 12 Oxford Street, Cambridge, MA 02138, USA From owner-molec-model@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!ibmh.msk.su!conf96 From: conf96@ibmh.msk.su ("IUBMB 96. Computational Biochemistry and Drug Design.") Newsgroups: bionet.molec-model Subject: conf.96 Date: 6 May 1996 08:47:35 -0700 Organization: Institute of Biomedical Chemistry, Acad of Med Sci Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net To whom it may concern: The Organizing Committee regret very much that IUBMB Conference "Computational Biochemistry and Drug Design" which was planned to be held in Russia in July 1996 is postponed for a year. Nowadays political and economical instability in Russia sharply restricts the organization of the Conference in July 1996. From more than 1000 first announcements being sent only 80 positive replies are received. However, no less than 200 participants are necessary for the leasing of the river ship. We explain it by the outcomes of parliamentary elections in 1995 and the forthcoming president's election in June 1996. In this situation IUBMB proposes to postpone the Conference for a year. We hope that the situation in Russia will be more favorable in 1997. The second announcement about the Conference will be sent to you in September-November 1996. Yours sincerely, Alexander Archakov Academician President of the Organizing Committee of IUBMB Conference on "Computational Biochemistry and Drug Design". -- IUBMB 1996. "Computational Biochemistry and Drug Design" Institute of Biomedical Chemistry Russian Academy of Medical Sciences Pogodinskaya St. 10, Moscow, 119832, Russia PHONE +007/095/245 0768 FAX +007/095/245 0857 E-MAIL conf96@ibmh.msk.su From owner-molec-model@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!newsfeed.internetmci.com!in2.uu.net!newsfeed.pitt.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!mm6n+ From: Marcella Madrid Newsgroups: bionet.molec-model Subject: Sequence Analysis workshops offered at the PSC Date: Tue, 7 May 1996 15:04:15 -0400 Organization: Pittsburgh Supercomputing Center, Carnegie Mellon, Pittsburgh, PA Lines: 122 Message-ID: NNTP-Posting-Host: po8.andrew.cmu.edu NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOPS FOR BIOMEDICAL RESEARCHERS PITTSBURGH SUPERCOMPUTING CENTER Biomedical Workshops offered by the Pittsburgh Supercomputing Center typically consist of theoretical lectures taught by leaders in the respective scientific discipline, and extensive hands-on computer sessions. During the computer sessions, participants are able to work on the examples provided or on their own experimental data. Attendance is limited to 20 participants to allow one-on-one instruction and encourage scientific interactions and discussions. Researchers nationwide are invited to apply. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu The following two Sequence Analysis workshops will be offered this summer: *********NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: June 9-14.************** Emphasis will be on alignment of and pattern extraction from multiple sequences. Topics to be discussed include Comparing and aligning sequences Identifying informative patterns in a set of sequences Using extracted informative patterns to identify related sequences. Leaders are: Dr. Gary Churchill, Cornell University; Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information: A limited number of grants to cover travel and/or hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Complimentary breakfast and lunches will be provided. APPLICATION DEADLINE: May 17, 1996. *****ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: August 25-28.****** Open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have appreciable experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for analyzing families and superfamilies of genes and proteins. Leaders are: Dr Stephen H. Bryant, National Center for Biotechnology Information, National Library of Medicine Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information : Hotel accommodations during the workshop for researchers affiliated with U.S. academic institutions will be paid by our NIH grant. Complimentary breakfast and lunches will also be provided. There is NO REGISTRATION FEE for this workshop. All other costs incurred in attending (travel, other meals, etc.) are the responsibility of the individual participant. APPLICATION DEADLINE: July 10, 1996. ********** PITTSBURGH SUPERCOMPUTING CENTER WORKSHOPS FOR BIOMEDICAL RESEARCHERS APPLICATION Workshop I am interested in attending:_______________________________________ Name: ______________________________________________________________ Affiliation: ______________________________________________________________ Address: ______________________________________________________________ (Business) ______________________________________________________________ ______________________________________________________________ (Home) ______________________________________________________________ Telephone: ____________________________ ____________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:_________________ Electronic Mail Address:_____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_______________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From owner-molec-model@net.bio.net Tue May 07 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Iosif Vaisman Newsgroups: bionet.molec-model Subject: ACS Course on Molecular Modeling: Methods and Techniques Date: 8 May 1996 11:58:02 -0700 Organization: The University of North Carolina at Chapel Hill Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net The American Chemical Society Short Course Molecular Modeling: Methods and Techniques Two Sessions: May 21-24, 1996 and August 20-23, 1996 Laboratory for Molecular Graphics and Theoretical Modeling College of Pharmacy, University of Texas at Austin Eleven previous four-day "hands-on" short courses have been offered with over 275 registrants from diverse backgrounds in the chemical, biological, and biomedical fields of research and teaching. Each student will have their own Silicon Graphics workstation and access to desktop computers for the duration of the short course. There will be daily "hands-on" laboratory sessions so YOU can work with state-of-the-art hardware and software. Topics: Molecular Mechanics Calculations, Molecular Mechanics Parameterization, Quantum Mechanics Calculations, Conformational Searching, Drug Design, Pharmacophore Development, 3D Databases, 3D Searching Strategies, and Combinatorial Chemistry Concepts Who Should Attend? Anyone wanting to know more about molecular structure calculations, pharmacophore design, 3D database searching, and structure-function relationships. The course has been designed primarily for experimental scientists in industry or academics with a background in the chemical, biological, and/or biomedical sciences. Software: MM2/MM3, SYBYL, INSIGHT/DISCOVER, QUANTA/CHARMm, SPARTAN, ISIS, CONCORD, CAChe, and more Lecturers J. Phillip Bowen (University of Georgia) Norman L. Allinger (University of Georgia) Dennis Liotta (Emory University) Alex Tropsha (University of North Carolina) Warren Hehre (Wavefunction, Inc.) Bob Pearlman (University of Texas at Austin) Osman Guner (Molecular Design) Call the ACS Education Services/Short Course Office at (800) 227-5558 or (202) 872-4508 or FAX (202) 872-6336 From owner-molec-model@net.bio.net Tue May 07 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Scott Le Grand Newsgroups: bionet.molbio.proteins,bionet.molec-model Subject: PDB3D Applet Date: 8 May 1996 12:59:06 -0700 Organization: University of California, Los Angeles Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <4moopp$1p1s@saba.info.ucla.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molbio.proteins:7838 bionet.molec-model:918 Hi guys, I have a Java applet that allows one to view PDB files... it's sitting at http://www.mbi.ucla.edu/people/legrand/pdb.html. I designed it specifically to allow people to incorporate PDB structures into web pages. It allows one to rotate and scale reasonably large molecules in real-time, much faster than anything else I've seen so far. I'm looking for feedback on what else it needs... Of course, you need a Java-capable browser to see the thing... Scott Le Grand From owner-molec-model@net.bio.net Wed May 08 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!netnews2.nwnet.net!news.u.washington.edu!verlinde From: verlinde@u.washington.edu (Christophe Verlinde) Newsgroups: bionet.molec-model Subject: SOFTWARE SPECIALIST JOB Date: 9 May 1996 00:51:43 GMT Organization: University of Washington Lines: 45 Message-ID: <4mrfiv$8ae@nntp3.u.washington.edu> NNTP-Posting-Host: saul7.u.washington.edu NNTP-Posting-User: verlinde At the Howard Hughes Medical Institute and the Biomolecular Structure Center of the University of Washington in Seattle an HHMI position is available for a SOFTWARE SPECIALIST in the group of Dr. Wim G.J. Hol, whose research is devoted to protein crystallography, structure based drug design, and protein engineering. Current projects focus on a variety of drug target proteins such as cholera toxin, trypanosomal enzymes, Fe-dependent repressors, topo- isomerases, multi-enzyme complexes, malaria drug targets and vaccine candidates, plus others. This multidisciplinary setting has a marvelous infrastructure for computational activities in crystal structure determination as well as in computer design and screening of novel protein inhibitors in the fields of infectious diseases and cancer. The position includes the development of new software, installation and maintenance of new software from outside sources, as well as introducing new group members to the computing environment, assisting in the installation and maintenance of an extensive network of computer systems, and participating in challenging ongoing crystallographic and modeling projects in the group. The ideal candidate is a person with experience in using and developing protein or small molecule crystallographic software, combined with a sincere interest in molecular modeling software for drug design. Good interpersonal skills are also essential. Please address applications, which should contain a full cv, a one-page summary of research and computing experience, and the full addresses plus telephone numbers of three references to: Wim G.J. Hol Ph.D. Howard Hughes Medical Institute and Biomolecular Structure Center University of Washington Box 357742 Seattle WA 98195-7742, USA Email: bmsc@gouda.bmsc.washington.edu HHMI is an Equal Opportunity Employer who offers a competitive salary and a full benefits program. From owner-molec-model@net.bio.net Thu May 09 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.kth.se!news From: Arne Elofsson Newsgroups: bionet.molec-model Subject: Professorship in Structural Biology Date: 10 May 1996 16:31:57 +0200 Lines: 75 Message-ID: NNTP-Posting-Host: rune.biokemi.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: September Gnus v0.77/XEmacs 19.13 STOCKHOLM UNIVERSITY FACULTY OF NATURAL SCIENCES PROFESSOR OF STRUCTURAL BIOCHEMISTRY Stockholm University invites applications for a position as Professor of Structural Biochemistry at the Faculty of Natural Sciences. The successful applicant will be a member of the Department of Biochemistry, one of the largest within the Faculty of Natural Sciences. The Department is involved in undergraduate teaching at all levels and has an extensive graduate program, at present involving 55 students. The research projects include Molecular Bioenergetics especially Photosynthesis (B. Andersson), Membrane Protein Insertion & Folding (G. von Heijne), Structure & Function of Proteins (M. Saraste), Biochemical Toxicology (J. DePierre), Protein Trafficing, Mitochondrial Biogenesis, Genetic Modification of Starch Biosynthesis and Nitrogen Fixation. The Department is well equipped and located with the other departments of chemistry and Life Sciences in the Arrhenius Laboratories for Natural Sciences. The Arrhenius Laboratories are situated in the northern part of the University Campus at Frescati, close to the centre of Stockholm. When appointing a professor at public universities in Sweden, emphasis is given to excellence in both research and teaching. Consideration is also given to administrative skills, in particular management. Proficiency in Swedish (Scandinavian) or English is necessary. The appointee will be expected to contribute to teaching at the undergraduate level as well as to the supervision of doctoral students. Salary is negotiable. The University is an Equal Opportunities employer, and since most professors at the Faculty of Natural Sciences are men, applications from female candidates are particularly welcome. Residence in the Stockholm area will be expected, at least after an initial start-up period. Informal inquiries may be made to professor Bertil Andersson, phone +46 8 16 29 10, e-mail bertil@biokemi.su.se or to the Head of the Department professor Stefan Nordlund, phone +46 8 16 29 32, e-mail stefan@biokemi.su.se Applications, quoting reference no 611-0000/96, should be sent to the Registrar, Staff Management Division, Stockholm University, S-106 91 Stockholm, Sweden. They must reach the Registrar's Office no later than 31 May 1996. The following items, all in four copies, should be included: 1. Curriculum vitae 2. Bibliography (numbered) 3. Description of the candidate's research achievements, teaching experience and management (5-10 pages). A guidance regarding the presentation of teaching qualifications may be obtained from Ulf Lindgren of the Staff Management Division, phone +46 8 16 33 22, fax +46 8 612 59 60. 4. Photocopies of relevant graduation diplomas. 5. Research publications of the candidate's own choice, numbered according to the bibliography. Items 1 and 2 should research the University before the application period expires. Items 3 and 4, and one copy of each item 5 should arrive no later than June 21, 1996. The three additional copies of item 5 are to be sent later, upon notification from the University, to the three Expert Members of the Appointment Board. -- ----------------------------------------------------------------- From: Arne Elofsson Email: arne@rune.biokemi.su.se Tel:+46(0)8-161553 WWW: http://www.biokemi.su.se/~arne/ From owner-molec-model@net.bio.net Fri May 10 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!news.datakom.su.se!usenet From: Arne Elofsson Newsgroups: bionet.molec-model Subject: MAC/PC Programs for Docking and Molecular Mechanics Date: 10 May 1996 12:49:13 +0200 Organization: Stockholm University Lines: 26 Message-ID: NNTP-Posting-Host: assar.biokemi.su.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: September Gnus v0.77/XEmacs 19.13 Hi. I'm sure this is a FAQ so please excuse me. We will teach a course in theoretical chemistry and we would need some easy to use molecular dynamics and docking tools. They have to run on a Mac or a PC (Windows). Any opinions ? arne ----------------------------------------------------------------- ! The danger with alcohol is that you get happy from it, and he ! ! who is happy does not need to drink. That is why you have to ! ! drink enough so that you can not remember that you have been ! ! happy, so that you can start over the next day. ! ----------------------------------------------------------------- -- ----------------------------------------------------------------- From: Arne Elofsson Email: arne@rune.biokemi.su.se Tel:+46(0)8-161553 WWW: http://www.biokemi.su.se/~arne/ From owner-molec-model@net.bio.net Sun May 12 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!bofh.dot!newsfeed.internetmci.com!csn!nntp-xfer-1.csn.net!magnus.acs.ohio-state.edu!jlabanow From: jlabanow@magnus.acs.ohio-state.edu (Jan K Labanowski) Newsgroups: bionet.molec-model Subject: ACES II/ab initio workshop in June (Gainesville, FL) Date: 13 May 1996 17:42:22 GMT Organization: The Ohio State University Lines: 15 Distribution: world Message-ID: <4n7s9u$pl5@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: bottom.magnus.acs.ohio-state.edu Rod Bartlett and the authors of ACES II are tentatively planning a fourth ACES II, and ab initio quantum chemistry workshop, to be held in June, at the University of Florida, Gainesville, FL. Through a cooperative arrangement with IBM, the workshop will be conducted on the new IBM 39H workstations. he tuition for the three and one-half day course is $500. Housing will be available at the Reitz Union hotel on campus at $30-40 a day. The intent of this message is to inquire whether there is sufficient interest to finalize the dates of the proposed workshop. Attendance is limited to 20 people. If interested, please contact aces2@qtp.ufl.edu." Denise Lindsay lindsay@qtp.ufl.edu From owner-molec-model@net.bio.net Mon May 13 23:00:00 1996 Path: biosci!biosci!not-for-mail From: torda@rsc.anu.edu.au (Andrew Torda) Newsgroups: bionet.molec-model,bionet.molecules.peptides,bionet.info-theory,bionet.molbio.proteins,sci.chem,bionet.structural-nmr Subject: Post-doc in computational chemistry, Canberra, Australia Date: 13 May 1996 22:07:01 -0700 Organization: Research School of Chemistry, Australian National University Lines: 69 Sender: daemon@net.bio.net Distribution: world Message-ID: <4n24rj$8v6@manuel.anu.edu.au> Reply-To: Andrew.Torda@anu.edu.au NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molec-model:925 bionet.molecules.peptides:314 bionet.info-theory:4122 bionet.molbio.proteins:7885 sci.chem:56139 bionet.structural-nmr:1276 POST DOCTORAL POSITION in Canberra, Australia with Andrew Torda Each year, the Research School of Chemistry at the Australian National University has a series of post-doctoral fellowships awarded on a competitive basis. Applications for the current round will be taken until about June 1, 1996. There are positions in several groups. The research group of Andrew Torda is oriented towards biomolecular calculation and simulation. We are working in areas such as low-resolution (protein fold recognition) force fields, refinement of experimental structures using MD simulation and lattice models of protein-lipid interactions. All the projects in the group involve coding - not just applications. It would be an advantage to have a reasonable knowledge of data structures and algorithms and programming experience in a civilized language (not fortran). Currently, possible projects would be centred around some new algorithms for aligning amino acid sequences to structures, based on the force fields we have developed. We are also looking at protein fold classification using topological and graph theory methods. Projects are negotiable. Salary is about A$38 000/year, initially for two years with a possible extension to a third year. The university will provide return air-fares to successful candidates and family. There is a housing office to help find accommodation. The Research School of Chemistry is part of the Institute of Advanced Studies which runs special research schools, in parallel to the normal teaching schools, and without any undergraduate teaching duties. The university is in the centre of Canberra (the nation's capital). Given the research orientation of the school, there is a lively academic environment. We have close contacts with the school's other theoretical groups in statistical mechanics, quantum chemistry and chemical physics. From the point of view of experimental groups, we maintain close ties to the school's NMR, X-ray crystallography and molecular biology groups. For further information about the possible projects of interest to the Torda group, contact Andrew Torda directly (Andrew.Torda@anu.edu.au) or slow mail: Andrew Torda, Research School of Chemistry Australian National University ACT, 0200 Australia or even fax: +61-6-249 0750 For information about the other groups and application forms, email the school secretary directly at schlsec@rsc.anu.edu.au and ask for a post-doctoral application pack to be mailed to you. To have a look at an uninformative home page with a low-resolution and uninteresting (but obligatory) photo, point your browser at http://rsc.anu.edu.au/~torda For the school's home page: http://rsc.anu.edu.au/Home.html From owner-molec-model@net.bio.net Tue May 14 23:00:00 1996 Path: biosci!GATE.SINICA.EDU.TW!ccchuang From: ccchuang@GATE.SINICA.EDU.TW (Chyh-Chong Chuang) Newsgroups: bionet.molec-model Subject: Use NMR structures for comparative modelling Date: 14 May 1996 18:05:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <1.5.4.32.19960515010409.006b9580@gate.sinica.edu.tw> NNTP-Posting-Host: net.bio.net I am curious how to use the NMR structures as the base stucture for comparative modelling using the avalible commecial packages, Homology, Composer,.. As I know, the NMR structures are low resolution. And usually the side chains are not well defined. Is it reasonable to use the average structure as the base structure? Is it reasonable to trnsfer the side chains' orientation to the conserved residues. Could anyone give me some suggest/comment about this practical question? Thanks all. ccchuang From owner-molec-model@net.bio.net Tue May 14 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.cais.net!bofh.dot!world1.bawave.com!newsfeed.internetmci.com!vixen.cso.uiuc.edu!usenet From: Andrew Dalke Newsgroups: bionet.molec-model Subject: ANNOUNCE: VMD version 1.1 is now available Date: Wed, 15 May 1996 06:30:55 -0500 Organization: University of Illinois at Urbana Lines: 131 Message-ID: <3199C06F.FF6@ks.uiuc.edu> NNTP-Posting-Host: juneau.ks.uiuc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP17) Announcing version 1.1 release of VMD --------------------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability version 1.1 of the program VMD, a package for the vizualization and analysis of biomolecular systems. This software is being made available to the structural biology research community free of charge, and includes the source code for VMD, documentation, and a precompiled binary for Silicon Graphics workstations running version 5 or later of the IRIX operating system. The postscript documentation (still being updated to include the new features in version 1.1) includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer such as Mosaic or Netscape. New in this version ------------------- This biggest improvement in version 1.1 is the development of scripting functions for molecular analysis and the 3D display of the results. These include: * Querying the internal VMD data base for information about a atom or set of atoms * Built-in functions for computing the center of mass, radius of gyration, etc. of an atom selection * Complete script control over atom position information * Adding and modifying graphical items (lines, spheres, etc.) in the display window to build user-defined scenes * Best (RMSD) fit alignment of molecules using the Kabsch method * Addition of Tcl-X and Tcl-DP * More control over internal VMD parameters * Vector and matrix routines for coordinate analysis Other improvements include: * Mouse controls for modifying the coordinates of an atom, residue or fragment (useful for structure building) * New rendering styles including cartoon * Orthographic perspective mode * New atom selection methods * Automatic secondary stucture determination (using STRIDE) * Ability to add forces to a molecular dynamics simulation * Support for the Radiance and ART ray tracers * Reduced levels of detail for faster visualization of complicated structures and, of course, many bug fixes. ============== Basic information about VMD =================== Obtaining VMD ------------- A more complete description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd (please see the README file in this directory for the latest version info) Email questions to vmd@ks.uiuc.edu. Features -------- VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. The program has many features, which include: o Many molecular rendering and coloring methods. o Stereo display capability. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). o Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files. o Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Rayshade, Raster3D, and Radiance. o Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis o Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code structure. o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: http://www.ks.uiuc.edu/Research/namd/ VMD can be used to set up and concurrently display a MD simulation using NAMD. The two programs, along with the intermediary communcations package (called MDComm) constitute the 'MDScope' environment. Availability ------------ VMD runs on Silicon Graphics workstations and may be compiled for HP-UX workstations if the NPGL library (a commercial port of the SGI GL library, available from Portable Graphics, Inc.) is available on your system, or to IBM 6000s with GL. Two versions of the distribution are available, one including the complete VMD source code, and one which just includes a precompiled VMD executable for SGI IRIX version 5.x. VMD, NAMD, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. For more information, see http://www.ks.uiuc.edu/Research/MDScope/ . This project is funded by the National Institutes of Health and the National Science Foundation. Andrew Dalke vmd@ks.uiuc.edu May 15, 1996 From owner-molec-model@net.bio.net Thu May 16 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Reto Koradi Newsgroups: bionet.structural-nmr,bionet.biophysics,bionet.molbio.proteins,bionet.molec-model,bionet.software,comp.graphics.visualization Subject: ANNOUNCE: MOLMOL 2.2.0 Date: 16 May 1996 20:59:01 -0700 Organization: Molekularbiologie & Biophysik, ETH Zurich Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <4ncvds$b84@elna.ethz.ch> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.structural-nmr:1287 bionet.biophysics:2021 bionet.molbio.proteins:7920 bionet.molec-model:930 bionet.software:15517 comp.graphics.visualization:7630 Release 2.2.0 of MOLMOL is now available. Check the web pages at: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ for detailed information, a list of changes, and instructions about downloading. Precompiled versions are available for SGI (IRIX 4.0.5 and 5.3), AIX, Digital UNIX, Solaris 2.4 and Linux. Source code is also available. MOLMOL is a program for display and analysis of macromolecular structures. It was developed as a joint project between BRUKER/Spectrospin and the group of Prof. Wuthrich at the Institut fuer Molekularbiologie und Biophysik, ETH Zurich. From owner-molec-model@net.bio.net Thu May 16 23:00:00 1996 Path: biosci!RUTCHEM.RUTGERS.EDU!jwest From: jwest@RUTCHEM.RUTGERS.EDU (John Westbrook) Newsgroups: bionet.molec-model Subject: New WWW Interface to the Nucleic Acid Database Date: 17 May 1996 13:40:49 -0700 Organization: Rutgers University Department of Chemistry Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: <319CE1B7.41C6@rutchem.rutgers.edu> NNTP-Posting-Host: net.bio.net New WWW Interface to the Nucleic Acid Database (NDB) --------------------------------------------------- The Nucleic Acid Database (NDB) Project assembles and distributes structural information about nucleic acids. It is a repository for the coordinates of nucleic acid-containing crystal structures and provides information of interest to researchers in the field, including standard geometry files for use in refinement and molecular modeling programs. The NDB can be accessed on the World Wide Web at: http://ndbserver.rutgers.edu/ and http://www.ebi.ac.uk/NDB/ (NDB mirror site at the European Bioinformatics Institute) A query interface that allows users to search the NDB is available at these WWW sites. The latest version of this interface provides several new options for using the database, including a full structure selection and report generation interface, a simple structure selection form for making quick selections, and a forms interface for creating status reports on the NDB holdings. Tutorials for using this interface are also available at these sites. We are very interested in getting your feedback. If you have any questions about the NDB or the new interface, or if you uncover a bug, please let us know by sending mail to ndbadmin@ndbserver.rutgers.edu. -- ****************************************************************** * John Westbrook Ph: (908) 445-4290 * * Department of Chemistry Fax: (908) 445-4320 * * Rutgers University * * PO Box 939 e-mail: jwest@ndb.rutgers.edu * * Piscataway, NJ 08855-0939 * ****************************************************************** From owner-molec-model@net.bio.net Thu May 16 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!baker From: baker@iastate.edu (Wayne R. Baker) Newsgroups: bionet.molec-model,bionet.structural-nmr,bionet.biophysics,sci.techniques.mag-resonance Subject: NMR Spectroscopist Position Available Date: 17 May 1996 20:56:07 GMT Organization: Biochemistry & Biophysics, Iowa State University Lines: 32 Message-ID: <4nip57$jnf@news.iastate.edu> Reply-To: hjfromm@iastate.edu NNTP-Posting-Host: pv0a0b.vincent.iastate.edu Xref: biosci bionet.molec-model:932 bionet.structural-nmr:1289 bionet.biophysics:2026 sci.techniques.mag-resonance:1658 The Department of Biochemistry and Biophysics, Iowa State University, seeks an NMR specialist to perform routine maintenance and to train users, as well as to design, implement and analyze experiments on a Varian Unity 500 NMR. A Ph.D. or the equivalent is required. Experience in biophysics, biochemistry or physical chemistry, along with expertise in current application of NMR to biological molecules is essential. Collaborative research using NMR and other biophysical techniques is encouraged. Send C.V. and three letters of reference to: Dr. Herbert J. Fromm c/o Stacey Poling Department of Biochemistry & Biophysics 1210 Molecular Biology Building Iowa State University Ames IA 50011-3260 Phone 515 294 6116 Deadline for receiving applications is June 30, 1996. For additional information about the Department and Iowa State University, see http://molebio.iastate.edu/bbhtml/homepage.htm Iowa State University is an Affirmative Action/Equal Opportunity Employer. Applications from women and minority candidates are especially encouraged. -- Wayne Baker (baker@iastate.edu) He who has a why to live for 4288 Molecular Biology Building can bear almost any how. Iowa State University --Nietzsche From owner-molec-model@net.bio.net Thu May 16 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!news.magg.net!news.bridge.net!uunet!in1.uu.net!amgen!usenet From: Greg Brown Newsgroups: bionet.molec-model Subject: 3-D to 2-D conversion of PDB files Date: Fri, 17 May 1996 16:44:20 -0600 Organization: Amgen Boulder Lines: 18 Message-ID: <319D0144.167E@amgen.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; U; IRIX 5.3 IP22) I am looking for a program that will convert a 3-D structure into a comprehensible 2-D representation. Many times a researcher can grasp a structure/function relationship more easily from a simplified 2-D drawing rather than a 3-D model that is printed out in 2-D paper. I am familiar with ligplot/hbplot and also with the recent paper by Barlow and Richards in J. Mol Graphics. Ligplot is too narrow in scope (generally just small regions of interactions are presented) and the non-linear mapping technique leaves many practical questions unanswered (like how do I do it!?). Any suggestions would be welcome, public domain or commercial programs. Thanks. -- Gregory S. Brown Molecular Structure/Protein Chemistry Amgen Boulder Mailstop AB-3A Boulder, CO. 80301 *** Disclaimer: These are the opinions of the poster not Amgen Inc.*** From owner-molec-model@net.bio.net Mon May 20 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!nostromo.bmc.uu.se!user From: gerard@xray.bmc.uu.se (Gerard Kleywegt) Newsgroups: bionet.software.x-plor,bionet.xtallography,bionet.structural-nmr,bionet.molec-model Subject: 8 Research Studentships (Structural Biology) available in Sweden Date: 20 May 1996 15:01:19 GMT Organization: Uppsala University Lines: 46 Message-ID: Reply-To: alwyn@xray.bmc.uu.se NNTP-Posting-Host: nostromo.bmc.uu.se X-Newsreader: Value-Added NewsWatcher 2.0d31h+ Xref: biosci bionet.software.x-plor:541 bionet.xtallography:2590 bionet.structural-nmr:1294 bionet.molec-model:935 SWEDISH STRUCTURAL BIOLOGY NETWORK ********************************** The Swedish Structural Biology Network is a five-year project funded by the Strategic Research Foundation with an annual budget of more than ten million Swedish Crowns. Its aim is to strengthen the strategic value of Structural Biology in Sweden. The Network consists of the Swedish academic centres involved in protein and DNA crystallography, NMR spectroscopy and modelling. The Network fosters collaboration in matters of research, education and knowledge transfer, and funds many new academic positions. At present, candidates are sought for 8 RESEARCH STUDENTSHIPS. Each position will be associated with a Swedish University, will be funded for a period of 4 years, and is expected to result in a doctoral dissertation. Candidates are required to have successfully completed undergraduate studies in a relevant area (e.g., molecular biology, biochemistry, biophysics). Studentships are available for the following research projects: (1) Structural studies on the Platelet-Derived Growth Factor Receptor and its complex with Platelet-Derived Growth Factor (X-ray) (2) Ribonucleotide Reductase holoenzyme complexes (X-ray) (3) Structure of viruses and viral components (X-ray) (4) Protein secretion (X-ray) (5) Ribosomal proteins and factors (X-ray) (6) Protein-protein interactions: structural studies of Bruton's Tyrosine Kinase(NMR) (7) Expression and NMR analysis of triply-labelled proteins (NMR) (8) Initiation of blood coagulation: interaction between Factor VII and Tissue Factor,and the role of non-catalytic domains (NMR) More information about these positions may be obtained from the Program Director: Prof. T.A. Jones, Department of Molecular Biology, Biomedical Centre, Uppsala University, Box 590, S-751 24 Uppsala (Fax: + 46 - 18 - 53 69 71, E-mail: alwyn@xray.bmc.uu.se). More information about the Structural Biology Network is availableon the World Wide Web, at URL: http://onyx.bmc.uu.se/~gerard/srf/srf.html Female candidates are expressly encouraged to apply. The closing date for applications is 15 June, 1996. -------------------------------------------------------------------- Gerard J. Kleywegt Department of Molecular Biology, Biomedical Centre Uppsala University, Uppsala, SWEDEN From owner-molec-model@net.bio.net Tue May 21 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!surfnet.nl!howland.reston.ans.net!news.cac.psu.edu!usenet From: userid@psu.edu (First M. Lastname) Newsgroups: bionet.molec-model,bionet.xtallography Subject: secondary to tertiary Date: 21 May 1996 21:22:01 GMT Organization: Penn State University Lines: 15 Sender: jdc6@0.0.0.0 Message-ID: <4ntc5p$186m@hearst.cac.psu.edu> NNTP-Posting-Host: thirtysixred.bmb.psu.edu X-Authinfo-User: jdc6@psu.edu X-Posted-From: InterNews 1.0.4@thirtysixred.bmb.psu.edu X-Authenticated: jdc6 on INN host 0.0.0.0 Xref: biosci bionet.molec-model:936 bionet.xtallography:2592 Dear Modelers, We have a protein for which the crystal structure has not been determined. Another protein from a family of which our protein is a member has had its crystal structure determined. Does anyone know of a program that I could use to make a prediction of the tertiary structure of our protein based on the comparison of the secondary structures of the two proteins mentioned above? Thanks in advance, Joe Callos Penn State U jdc6@email.psu.edu From owner-molec-model@net.bio.net Tue May 21 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.molec-model,bionet.xtallography Subject: Re: secondary to tertiary Date: Wed, 22 May 1996 09:15:00 +0100 Organization: U. Texas-Houston Lines: 32 Message-ID: References: <4ntc5p$186m@hearst.cac.psu.edu> NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit Xref: biosci bionet.molec-model:937 bionet.xtallography:2595 In article <4ntc5p$186m@hearst.cac.psu.edu>, userid@psu.edu (First M. Lastname) wrote: > We have a protein for which the crystal structure has not been > determined. Another protein from a family of which our protein is a > member has had its crystal structure determined. > Does anyone know of a program that I could use to make a prediction of > the tertiary structure of our protein based on the comparison of the > secondary structures of the two proteins mentioned above? Two suggestions: 1. submit your sequence to SWISS-Model http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html P.S.: If you have not written a letter of support for SWISS-Prot database, please do so because SWISS-PROT is facing a possible closure. See info at: http://expasy.hcuge.ch/sprot/help-sprot.html 2. You can get Modeller from Dr. Andrej Sali http://guitar.rockefeller.edu/ftp/pub/modeller/modeller3.README MODELLER PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Good luck, T. Chyau Liang U. Texas-Houston From owner-molec-model@net.bio.net Tue May 21 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!newsreader.sprintlink.net!news.hscsyr.edu!newsadm From: Tom Duncan Newsgroups: bionet.molec-model Subject: Rendering Software Date: Wed, 22 May 1996 11:27:06 -0700 Organization: SUNY Health Science Ctr, Dept Biochemistry Lines: 9 Message-ID: <31A35C7A.41C6@cross.bmb.hscsyr.edu> NNTP-Posting-Host: cross.bmb.hscsyr.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) I am interested in Raster3D, Rayshade, or a similar rendering package, but I need to find a pre-compiled version for IRIX5.3. Thanks. -- Thomas M. Duncan Dept. Biochemistry & Molecular Biology SUNY Health Science Center 750 E Adams St, Syracuse, NY 13210 Email: duncant@vax.cs.hscsyr.edu or duncant@cross.bmb.hscsyr.edu From owner-molec-model@net.bio.net Thu May 23 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!magnus.acs.ohio-state.edu!news.cis.ohio-state.edu!nntp.sei.cmu.edu!bb3.andrew.cmu.edu!newsfeed.pitt.edu!gvls1!news.cse.psu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!usenet.eel.ufl.edu!bofh.dot!usenet.cis.ufl.edu!usenet.ufl.edu!mitzi.rsmas.miami.edu!news.ir.miami.edu!impala.ir.miami.edu!clp2gq11 From: Soomi Pyo Newsgroups: bionet.molec-model Subject: Looking for "Explorer" user Date: Fri, 24 May 1996 14:43:19 -0400 Organization: University of Miami (IR) Lines: 8 Message-ID: NNTP-Posting-Host: impala.ir.miami.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I'm looking for explorer users. It's one of the Silicon Graphic Computer software. If anybody is familiar, I'd like to talk. Thank you. Soomi. From owner-molec-model@net.bio.net Mon May 27 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!swrinde!cssun.mathcs.emory.edu!news-feed-1.peachnet.edu!news.cc.emory.edu!usenet From: "Keith D. Wilkinson" Newsgroups: bionet.xtallography,bionet.molec-model Subject: DIRECTOR, Molecular Graphics at Emory Date: Tue, 28 May 1996 18:13:08 +0000 Organization: Emory University Lines: 42 Message-ID: <31AB4234.1F15@bimcore.emory.edu> Reply-To: genekdw@bimcore.emory.edu NNTP-Posting-Host: genekdw.dialup.emory.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) Xref: biosci bionet.xtallography:2617 bionet.molec-model:940 Director of Molecular Graphics Biomolecular Computing Resource Emory University The Emory University Biomolecular Computing Resource (BIMCORE) seeks a Ph.D. in Chemistry or the Biological Sciences with training and at least two years experience in molecular graphics, including SYBYL, KINEMAGE, RASMOL, and INSIGHT. An academic appointment is possible for qualified candidates. The Director of Molecular Graphics will be responsible for all aspects of the BIMCORE Molecular Graphics Facility, including software selection and upgrades, education (user training and courses in Molecular Graphics), new software development, networking and hardware maintenance. The Facility includes a networked cluster of SGI workstations and will serve approximately 25 laboratories at Emory University and furnish expertise related to the graphical display and analysis of the structure of biological molecules. BIMCORE is a high-end computing/graphics facility supporting talented researchers and students at Emory University. The facility provides software and user support as well as training in the use of genetic data analysis software and molecular modeling and graphics of biological molecules. Emory University is a private institution located in suburban Atlanta adjacent to the Centers for Disease Control, The American Cancer Society, Yerkes Primate Center and the Veterans Administration Medical Center. This campus includes the Woodruff Health Sciences Center, a hospital system serving a population base of over 3 million, an outstanding faculty, and a highly-competitive student body. The Biomedical research programs occupy over 500,000 square feet of new or renovated research space and garner in excess of $100 million per year in peer-reviewed research support. Applications will be accepted until the position is filled. Direct Inquiries to: Scott Sammons, BIMCORE Director 3025 Rollins Research Center Emory University Atlanta, GA, 30322 Email sammons@bimcore.emory.edu Voice (404)727-2780 Fax (404)727-3659 From owner-molec-model@net.bio.net Tue May 28 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!nntp.uio.no!usenet From: larsn@bio.uio.no (Lars Norderhaug) Newsgroups: bionet.molec-model Subject: Antibody Modelling Date: 29 May 1996 18:30:57 GMT Organization: Uninversity of Oslo Lines: 10 Message-ID: <4oi551$6o3@ratatosk.uio.no> NNTP-Posting-Host: xyplex15.uio.no Mime-Version: 1.0 X-Newsreader: WinVN 0.93.14 I want to modell the CDR regions of an antibody to enhance the affinity for a protein antigen. Only the sequence of the antibody is known not the crystal structure. Can anyone suggest a specialized program for antibody modelling that works under Irix 5.3. Lars Norderhaug larsn@bio.uio.no From owner-molec-model@net.bio.net Wed May 29 23:00:00 1996 Path: biosci!agate!cgl!friedman From: friedman@cgl.ucsf.edu (Simon Friedman) Newsgroups: bionet.molec-model Subject: Re: Antibody Modelling Date: 30 May 1996 08:26:29 GMT Organization: Computer Graphics Laboratory, UCSF Lines: 39 Message-ID: <4ojm3l$53i@cgl.ucsf.edu> References: <4oi551$6o3@ratatosk.uio.no> NNTP-Posting-Host: socrates.ucsf.edu In article <4oi551$6o3@ratatosk.uio.no> larsn@bio.uio.no (Lars Norderhaug) writes: >I want to modell the CDR regions of an antibody to enhance the affinity >for a protein antigen. Only the sequence of the antibody is known not >the crystal structure. > >Can anyone suggest a specialized program for antibody modelling that >works under Irix 5.3. > >Lars Norderhaug >larsn@bio.uio.no > I believe that Oxford Molecular marketed a program for modeling Antibody structures at some point. Hope this helps. Simon friedman@cgl.ucsf.edu From owner-molec-model@net.bio.net Wed May 29 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.rediris.es!power.ci.uv.es!quififar6!ramon.garcia From: ramon.garcia@uv.es (Ramon Garcia Domenech) Newsgroups: bionet.molec-model Subject: Help about babel Date: Thu, 30 May 1996 13:16:40 +1000 Organization: Universitat de Valencia Lines: 5 Message-ID: NNTP-Posting-Host: quififar6.quifis.uv.es X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] We are interested in the acquisition of a program for the change of format of molecular graphics files (for example Babel). We only know the existence of that program. We request any information about commercial availability of these kind of programs. Please send us the information via E-mail. From owner-molec-model@net.bio.net Wed May 29 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!homer.alpha.net!news.ultranet.com!usenet.eel.ufl.edu!bofh.dot!warwick!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Phil Biggin Newsgroups: bionet.molec-model Subject: Re: Help about babel Date: Thu, 30 May 1996 13:18:13 +0100 Organization: Oxford University Lines: 36 Message-ID: <31AD9205.2781@biop.ox.ac.uk> References: NNTP-Posting-Host: bundle.biop.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX64 6.1 IP26) To: Ramon Garcia Domenech CC: phil@biop.ox.ac.uk Ramon Garcia Domenech wrote: > > We are interested in the acquisition of a program for the change of format of > molecular graphics files (for example Babel). > We only know the existence of that program. We request any information about > commercial availability of these kind of programs. > Please send us the information via E-mail. You can get babel for free as far as I know from :- anonymous ftp at :- ccl.osc.edu in the directory :- /pub/chemistry/software/UNIX/babel or you can visit the babel site :- http://mercury.aichem.arizona.edu/babel.html Hope this helps, Phil -- Phil Biggin phil@biop.ox.ac.uk Molecular Biophysics voice: +44 865 275380 University of Oxford fax: +44 865 275182 South Parks Road http://indigo1.biop.ox.ac.uk/phil/phil.html Oxford OX1 3QU From owner-molec-model@net.bio.net Wed May 29 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!news.emi.com!pauling.wadsworth.org!usenet From: Mark Rosenberg Newsgroups: bionet.molec-model Subject: Re: Looking for "Explorer" user Date: 30 May 1996 15:07:43 GMT Organization: Wadsworth Center, NY Health Dept. Lines: 9 Message-ID: <4okdjv$4rm@pauling.wadsworth.org> References: NNTP-Posting-Host: alcor.wadsworth.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP22) X-URL: news:Pine.ULT.3.92.960524143905.5109A-100000@impala.ir.miami.edu I know somebody that uses it in UK- Jeremy.Derreck@umist.ac.uk or Jeremy.Dereck@umist.ac.uk Anyway it is Jeremy Dereck at The Dept of Biochemistry and AMB at Umist Po BOX 88, M60 1 QD, Uk I am not sure how spell his last name hence 2 e.mail address. Mark From owner-molec-model@net.bio.net Wed May 29 23:00:00 1996 Path: biosci!ARSERRC.GOV!GKING From: GKING@ARSERRC.GOV (Gregory King) Newsgroups: bionet.molec-model Subject: superimposing molecules Date: 30 May 1996 09:21:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <6221171230051996.A58995.CERES.11A5F3111500*@MHS> NNTP-Posting-Host: net.bio.net Greetings, I'm looking for software (or an explanation of an efficient algorithm) that will superimpose molecule A onto molecule B with a combination of translations and rotations, and using a minimal rms deviation as the convergence criterion. There is a known one-to-one correspondence between the relevant atoms in both molecules (I'll be comparing peptides, and using the backbone atoms as the relevant ones). Thanks in advance. Greg King gking@arserrc.gov From owner-molec-model@net.bio.net Wed May 29 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dish.news.pipex.net!pipex!dircon!not-for-mail From: ahenry@oxmol.co.uk (Andrew Henry) Newsgroups: bionet.molec-model Subject: Re: Antibody Modelling Date: 30 May 1996 15:32:13 +0100 Organization: Oxford Molecular Lines: 25 Sender: ahenry@tdc.dircon.co.uk Message-ID: <4okbhd$ega@tdc.dircon.co.uk> References: <4oi551$6o3@ratatosk.uio.no> <4ojm3l$53i@cgl.ucsf.edu> Reply-To: ahenry@oxmol.co.uk (Andrew Henry) NNTP-Posting-Host: tdc.dircon.co.uk In article <4ojm3l$53i@cgl.ucsf.edu>, Simon Friedman wrote: >In article <4oi551$6o3@ratatosk.uio.no> larsn@bio.uio.no (Lars Norderhaug) writes: >>I want to modell the CDR regions of an antibody to enhance the affinity >>for a protein antigen. Only the sequence of the antibody is known not >>the crystal structure. >>Can anyone suggest a specialized program for antibody modelling that >>works under Irix 5.3. >I believe that Oxford Molecular marketed a program >for modeling Antibody structures at some point. >Hope this helps. I work for Oxford Molecular as an antibody modeller. For more information about our antibody modelling software (AbM), see: http://www.oxmol.co.uk/PRODUCTS/abm_top.html -- Andrew Henry Oxford Molecular ahenry@oxmol.co.uk From owner-molec-model@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!sdd.hp.com!night.primate.wisc.edu!ames!cnn.nas.nasa.gov!splatter.nas.nasa.gov!bross From: bross@splatter.nas.nasa.gov (Wilson S. Ross) Newsgroups: bionet.molec-model Subject: Re: superimposing molecules Date: 30 May 1996 20:48:56 GMT Organization: NAS/NASA Ames Research Center Lines: 10 Distribution: world Message-ID: <4ol1jo$m56@cnn.nas.nasa.gov> References: <6221171230051996.A58995.CERES.11A5F3111500*@MHS> NNTP-Posting-Host: splatter.nas.nasa.gov [rms fit of topologically identical structures] Kabsch, (1976) Acta Cryst. A32, 922-923 and (1978) Acta Cryst. A34, 827-828. I believe there may be a more recent method that is slightly more elegant. My structure/trajectory analysis program Carnal in AMBER uses Kabsch, but it's just a small part of a large (tho cheap) pkg (http://www.amber.ucsf.edu/amber/). Bill Ross From owner-molec-model@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!bofh.dot!tank.news.pipex.net!pipex!oleane!jussieu.fr!moka.ccr.jussieu.fr!not-for-mail From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN) Newsgroups: bionet.molec-model Subject: Re: superimposing molecules Date: 31 May 1996 09:16:56 +0200 Organization: CCR - Universites Paris VI/VII - Paris - France Lines: 21 Message-ID: <4om6d8$4go5@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 References: <6221171230051996.A58995.CERES.11A5F3111500*@MHS> >I'm looking for software (or an explanation of an efficient algorithm) that >will superimpose molecule A onto molecule B with a combination of translations >and rotations, and using a minimal rms deviation as the convergence criterion. >There is a known one-to-one correspondence between the relevant atoms in both >molecules (I'll be comparing peptides, and using the backbone atoms as the >relevant ones). The r.m.s. method is called the Procuste (or Procrustes) algorithm. The optimal rotation and translation are known analytically. It is described in J.Comput.Chem. 1995,16[1],80-90 (appendix 3). If you need an algorithm working with different molecules (i.e. there is no correspondence between atoms, and the number of atoms are not equal), I have written a programme doing that. Capabilities are around some thousands of atoms. Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, URA34), ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse, Phone: +33 (1) 44 27 48 57 75005 Paris, France. FAX : +33 (1) 45 84 98 25 From owner-molec-model@net.bio.net Fri May 31 23:00:00 1996 Newsgroups: bionet.molec-model Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!tank.news.pipex.net!pipex!usenet1.news.uk.psi.net!uknet!uknet!bcc.ac.uk!martin From: martin@bsm.bioc.ucl.ac.uk (Andrew Martin) Subject: Re: Antibody Modelling Message-ID: <1996May31.132239.51157@ucl.ac.uk> Date: Fri, 31 May 1996 13:22:39 GMT References: <4oi551$6o3@ratatosk.uio.no> <4ojm3l$53i@cgl.ucsf.edu> Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Lines: 38 Simon Friedman (friedman@cgl.ucsf.edu) wrote: : In article <4oi551$6o3@ratatosk.uio.no> larsn@bio.uio.no (Lars Norderhaug) writes: : >I want to modell the CDR regions of an antibody to enhance the affinity : >for a protein antigen. Only the sequence of the antibody is known not : >the crystal structure. : > : >Can anyone suggest a specialized program for antibody modelling that : >works under Irix 5.3. : > : >Lars Norderhaug : >larsn@bio.uio.no : > : I believe that Oxford Molecular marketed a program : for modeling Antibody structures at some point. : Hope this helps. Hi, I'm the original academic author of the loop modelling part of the code in Oxford Molecular's AbM package. I'd recommend this as the best automated prcocedure around, though it does have a few problems (which are fine providing you know about them). Take a look at my Web page for lots more info on antibodies. Mail me if you want more info. Best wishes, Andrew -- **************************************************************************** Dr. Andrew C.R. Martin, University College London & SciTech Software EMAIL: martin@biochem.ucl.ac.uk Tel:(Work) +44(0)171 419 3890 URL: http://www.biochem.ucl.ac.uk/~martin (Home) +44(0)1372 275775 ****************************************************************************