From owner-molec-model@net.bio.net Mon Jan 02 22:00:00 1995 Newsgroups: bionet.molec-model Path: biosci!agate!howland.reston.ans.net!news.starnet.net!wupost!csus.edu!netcom.com!dougnb From: dougnb@netcom.com (Doug Neubauer) Subject: Molecular Dynamics (specific heat) Message-ID: Organization: NETCOM On-line Communication Services (408 261-4700 guest) Date: Tue, 3 Jan 1995 08:56:45 GMT Lines: 24 Hello. I am working through the section in Allen-Tildesley on calculating properties from RMS fluctuations. In particular, specific heat, Cv, from fluctuations in potential (or kinetic) energy. This works fine in the NVE ensemble, however I am attempting to use Berendsen's external bath technique to generate a constant pressure and temperature. According to the 1984 article the ensemble is undefined and therefore the fluctuation data is invalid. (Which I verified, neither Cv or Cp were correct) So what I ended up doing is using the coupling bath to establish the target temperature/pressure then turn off the bath in order to generate correct RMS fluctuation data. Unfortunately the pressure (and temperature) tend to wander away from the target values. Could someone point me to more recent literature which might have a better way to do this. Ideally, I would like to get the specific heat value without having to turn off the external bath. Thanks in advance. Doug Neubauer From owner-molec-model@net.bio.net Tue Jan 03 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!spool.mu.edu!uwm.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!axe1!axelsen From: axelsen@axe1 (Paul H Axelsen) Newsgroups: sci.techniques.spectroscopy,bionet.biophysics,sci.research,bionet.molec-model,bionet.general Subject: Re: Unusual Postdoctoral Opportunity Available Followup-To: sci.techniques.spectroscopy,bionet.biophysics,sci.research,bionet.molec-model,bionet.general Date: 4 Jan 1995 13:33:22 GMT Organization: University of Pennsylvania Lines: 13 Distribution: world Message-ID: <3ee832$5vp@netnews.upenn.edu> References: <3ec49f$f19@netnews.upenn.edu> <3ecd4i$bs6@oak.oakland.edu> NNTP-Posting-Host: axe1.med.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] Xref: biosci sci.techniques.spectroscopy:1028 bionet.biophysics:573 sci.research:3501 bionet.molec-model:218 bionet.general:12686 Please respond to this posting by Email or phone, as it is a bit unusual for me to be keeping up with these newsgroups. --------------------- axe@pharm.med.upenn.edu -------------------------------- Paul H. Axelsen MD .... .... . . . . 215-898-9238 (ofc) Department of Pharmacology . . . .. . .. . 215-898-9766 (lab) University of Pennsylvania .... ... . . . . . . 215-573-2236 (fax) 3620 Hamilton Walk . . . .. . .. 610-293-1659 (home) Philadelphia, PA 19104-6084 . .... . . . . ------------------------------------------------------------------------------ From owner-molec-model@net.bio.net Tue Jan 03 22:00:00 1995 Newsgroups: bionet.molec-model Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!convex!insosf1.infonet.net!solaris.cc.vt.edu!news.alpha.net!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!uunet!news.unr.edu!ub!acsu.buffalo.edu!ubvms.cc.buffalo.edu!vp19wqa3 From: vp19wqa3@ubvms.cc.buffalo.edu (Yao S. Ko) Subject: looking for HBPLUS www site Message-ID: News-Software: VAX/VMS VNEWS 1.50AXP Sender: vp19wqa3@ubvms.cc.buffalo.edu (Yao Sen Ko) Nntp-Posting-Host: ubvmsa.cc.buffalo.edu Organization: University at Buffalo Date: Wed, 4 Jan 1995 18:09:00 GMT Lines: 10 Hi, I should greatly appreciate if anyone can tell me the URL for the HBPLUS www site. Thanks in advance! =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Yao S. Ko vp19wqa3@ubvms.cc.buffalo.edu Space, the final ... parking place! =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-molec-model@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!rutgers!utcsri!yonge.cs.toronto.edu!neuron.ai.toronto.edu!ai.toronto.edu!steeg Newsgroups: bionet.software,bionet.molbio.proteins,bionet.molec-model From: steeg@cs.toronto.edu ("Evan W. Steeg") Subject: Pictures/coordinates for states in protein folding Message-ID: <95Jan4.201837edt.280@neuron.ai.toronto.edu> Originator: root@yonge.cs.toronto.edu Nntp-Posting-Host: yonge.cs.toronto.edu Organization: CS Lab, University of Toronto Distribution: bionet Date: 5 Jan 95 01:19:19 GMT Lines: 37 Xref: biosci bionet.software:10540 bionet.molbio.proteins:3368 bionet.molec-model:220 A friend of mine would like some pictures of a protein in several different states of folding/unfolding. She'd really prefer Cytochrome C, but other proteins would suffice. Otherwise, her needs are very flexible: -- Intermediate states may be observed (NMR, etc.) or modelled (according to some accepted classical/qm simulation model). -- Pictures may be space-filling, or ribbon diagrams, or etc. -- Pictures in any unix-friendly format (gif, tiff, ppm, etc.) In addition to or in lieu of graphics, perhaps there is a database of partially-folded structures somewhere, akin to the brookhaven pdb of folded structure coordinate files? I'm curious about this myself. Last but not least, can anyone recommend offhand a particularly good paper on some theoretical or empirical aspects of folding that features a sequence of pictures as described above (especially of Cyt C!) ? Thanks for any pictures, pointers, or references! If I discover anything especially interesting, I'd be glad to summarize and repost. Regards, Evan Evan W. Steeg (416) 978-5182 steeg@ai.toronto.edu Dept of Computer Science steeg@t13.lanl.gov University of Toronto, Toronto, Canada M5S 1A4 FAX: (416) 978-1455 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- "We tend to scoff at the beliefs of the ancients. But we can't scoff at them personally, to their faces, and this is what annoys me." - Jack Handey =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From owner-molec-model@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!rutgers!utcsri!yonge.cs.toronto.edu!neuron.ai.toronto.edu!ai.toronto.edu!steeg Newsgroups: bionet.software,bionet.molbio.proteins,bionet.molec-model From: steeg@cs.toronto.edu ("Evan W. Steeg") Subject: Re: Pictures/coordinates for states in protein folding Message-ID: <95Jan5.175343edt.850@neuron.ai.toronto.edu> Originator: root@yonge.cs.toronto.edu Nntp-Posting-Host: yonge.cs.toronto.edu Organization: CS Lab, University of Toronto References: <95Jan4.201837edt.280@neuron.ai.toronto.edu> Distribution: bionet Date: 5 Jan 95 22:54:35 GMT Lines: 53 Xref: biosci bionet.software:10554 bionet.molbio.proteins:3376 bionet.molec-model:222 If I may just follow up on my own posting of yesterday: In article <95Jan4.201837edt.280@neuron.ai.toronto.edu>, Evan W. Steeg wrote: > A friend of mine would like some pictures of a protein in several >different states of folding/unfolding. She'd really prefer Cytochrome C, >but other proteins would suffice. Otherwise, her needs are very >flexible: > > -- Intermediate states may be observed (NMR, etc.) or modelled (according > to some accepted classical/qm simulation model). > > -- Pictures may be space-filling, or ribbon diagrams, or etc. > > -- Pictures in any unix-friendly format (gif, tiff, ppm, etc.) > > In addition to or in lieu of graphics, perhaps there is a database >of partially-folded structures somewhere, akin to the brookhaven pdb >of folded structure coordinate files? I'm curious about this myself. > > Last but not least, can anyone recommend offhand a particularly good >paper on some theoretical or empirical aspects of folding that features >a sequence of pictures as described above (especially of Cyt C!) ? > 1. Lest there be any confusion... what I meant when I referred to various states of folding/unfolding was *well-characterized intermediates in the folding pathway*, and not "unfolded" or "random" configurations. Obviously, it makes no sense to have a database of "unfolded" protein coordinates. 2. I'm making this request for a friend who wants to do a research/reading project for a chemistry course. I talked her into being interested in the protein folding problem (oops) and she is already thinking of how she might give her presentation if she does follow through on this nontrivial topic. It would be nice if she could put up a couple of slides graphically illustrating the ("real" or hypothesized) folding of a particular protein. 3. It occurs to me that, besides my friend's immediate needs, it may be of interest to others (myself included) if there exists any database of either graphics (e.g., a WWW site) or databases of proposed or discovered intermediate structures. Thanks again for your attention. -- Evan Evan W. Steeg (416) 978-5182 steeg@ai.toronto.edu Dept of Computer Science steeg@t13.lanl.gov University of Toronto, Toronto, Canada M5S 1A4 FAX: (416) 978-1455 From owner-molec-model@net.bio.net Wed Jan 04 22:00:00 1995 Path: biosci!biophy.jussieu.fr!michel From: michel@biophy.jussieu.fr (Michel SEIGNEURET) Newsgroups: bionet.molec-model Subject: re:looking for HBPLUS www site Date: 5 Jan 1995 08:21:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9501051627.AA07819@mood.biophy.jussieu.fr> NNTP-Posting-Host: net.bio.net Hi, Why don't you try: http://bsmcha1.biochem.ucl.ac.uk/~mcdonald/hbplus/home.html Good luck. Michel From owner-molec-model@net.bio.net Thu Jan 05 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!redstone.interpath.net!mercury.interpath.net!not-for-mail From: morgan@mercury.interpath.net (Morgan Ryan) Newsgroups: bionet.molec-model Subject: pdb->dxf or anything else? Date: 5 Jan 1995 21:06:14 -0500 Organization: Interpath -- Public Access UNIX for North Carolina Lines: 4 Message-ID: <3ei8im$rff@mercury.interpath.net> NNTP-Posting-Host: mercury.interpath.net Is there a utility that will convert pdb files to dxf or any other 3d format? (Mac preferred). I'm trying to move molecular graphics to Ray Dream Designer...Thanks. Morgan Ryan From owner-molec-model@net.bio.net Sun Jan 08 22:00:00 1995 Path: biosci!ARGO.URV.ES!pujadas From: pujadas@ARGO.URV.ES (Gerard Pujadas BQ 2253) Newsgroups: bionet.molec-model Subject: Mac Mollecular Moldelling Soft Date: 9 Jan 1995 00:51:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9501090849.AA22690@quimica.urv.es> NNTP-Posting-Host: net.bio.net Hi, my name is Gerard Pujadas and I am looking for a cheap Mollecular Modelling program for Macintosh. Does anybody know a program of this characte- ristics? Thanks and good year to all the netters. Gerard Pujadas Dept. Bioquimica i Biotecnologia Universitat Rovira i Virgili Plac,a Imperial Tarraco 1 43005 Tarragona (CATALONIA) Europe. e-mails: pujadas@quimica.urv.es utabbt01@cadi.cesca.es telf: (34 77) 55 95 65 From owner-molec-model@net.bio.net Sun Jan 08 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!news.sprintlink.net!sundog.tiac.net!mpp.tiac.net!terra From: terra@tiac.net (Ophira Rosolio Aharonson) Newsgroups: bionet.molec-model Subject: Journal of Computational chemistry Date: Mon, 9 Jan 1995 17:15:51 Organization: Terra Computers Inc. Lines: 4 Message-ID: NNTP-Posting-Host: mpp.tiac.net X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Wanted: contact for Journal of Computational chemistry. Thanks Ophira Rosolio-Aharonson Terra@Computers Inc. terra tiac.net From owner-molec-model@net.bio.net Mon Jan 09 22:00:00 1995 Path: biosci!daresbury!s-crim1!mbasd From: mbasd@s-crim1.dl.ac.uk (A. Sheppard) Newsgroups: bionet.molec-model Subject: Oral availability of drugs... Date: 10 Jan 1995 13:50:51 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 33 Distribution: bionet Message-ID: <3eu3br$c3g@mserv1.dl.ac.uk> NNTP-Posting-Host: s-crim1.dl.ac.uk X-Newsreader: TIN [version 1.2 PL2] Dear Readers, I would be grateful for comments, ideas, anecdotes, references etc. on the following topic: In the area of drug research, a frequent problem which arises is that of obtaining oral-availability: it is usually more desirable to have an orally active compound than one which is active only when injected. What I want to know is the following: 1 Is it possible to predict whether a compound will be orally active? 2 On observing a compound has little or no oral activity, are there any structural modifications which can be used to increase the oral activity of the compound? 3 Is it possible to use an adjuvant to increase the absorption of a weakly orally active compound? 4 Are there any in vitro test systems which will predict whether a compound is orally active? If there are such test systems, are they available commercially or have they been devloped in-house? I will summarise useful information to the net. Andy Sheppard Ferring Research Institute mbasd@seqnet.dl.ac.uk [crossposted to newsgroups bionet.general, bionet.molbio.methds-reagnts, bionet.molec-model and the Computational Chemistry list] From owner-molec-model@net.bio.net Mon Jan 09 22:00:00 1995 Newsgroups: bionet.molec-model Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!Germany.EU.net!EU.net!sun4nl!ruuinf!ruu.nl!usenet From: Ton Rullmann Subject: Re: pdb->dxf or anything else? Message-ID: <1995Jan10.134636.7290@cc.ruu.nl> Sender: usenet@cc.ruu.nl Organization: ACCU References: <3ei8im$rff@mercury.interpath.net> Date: Tue, 10 Jan 1995 13:46:36 GMT Lines: 42 morgan@mercury.interpath.net (Morgan Ryan) wrote: > > Is there a utility that will convert pdb files to dxf or any other 3d > format? (Mac preferred). I'm trying to move molecular graphics to Ray > Dream Designer...Thanks. Morgan Ryan You may want to try the Babel program suite, developed by the Dolata Research Group, University of Arizona. Babel will read the following file types : Alchemy AMBER PREP Ball and Stick Biosym .CAR Boogie Cacao Cartesian Cambridge CADPAC CHARMm Chem3D Cartesian 1 Chem3D Cartesian 2 CSD CSSR CSD FDAT CSD GSTAT Free Form Fractional GAMESS Output Gaussian Z-Matrix Gaussian Output Hyperchem HIN Mac Molecule Macromodel Micro World MM2 Input MM2 Ouput MM3 MMADS MDL MOLfile MOLIN Mopac Cartesian Mopac Internal Mopac Output PDB Quanta ShelX Spartan Sybyl Mol Sybyl Mol2 XYZ Babel will write the following file types : Alchemy Ball and Stick Cacao Cartesian CAChe MolStruct Chem3D Cartesian 1 Chem3D Cartesian 2 ChemDraw Conn. Table CSD CSSR Gamess Input Gaussian Cartesian Gaussian Z-matrix Hyperchem HIN IDATM Mac Molecule Macromodel Micro World MM2 Input MM2 Ouput MM3 MMADS MDL Molfile Mopac Cartesian Mopac Internal PDB Report Spartan Sybyl Mol Sybyl Mol2 XYZ Babel is available via annonymous ftp from joplin.biosci.arizona.edu in pub/Babel. Hope this helps. Ton Rullmann. From owner-molec-model@net.bio.net Tue Jan 10 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!hudson.lm.com!newsfeed.pitt.edu!uunet!ankh.iia.org!babbage.ece.uc.edu!ucunix.san.uc.edu!ucunix.san.uc.edu!not-for-mail From: naussjl@ucunix.san.uc.edu (Jeffrey L Nauss) Newsgroups: bionet.molec-model Subject: AMBER Parameters for Ba2+ and Sr2+ Date: 10 Jan 1995 17:03:21 -0500 Organization: University of Cincinnati Lines: 10 Message-ID: <3ev079$6eo@ucunix.san.uc.edu> NNTP-Posting-Host: ucunix.san.uc.edu X-Newsreader: TIN [version 1.2 PL2] Would anyone happen to have parameters for the AMBER forcefield for the ions Ba2+ and Sr2+? The actual parameters or a reference would be helpful. Thanks in advance. -- Jeff Nauss Texas A&M Class of '77 Department of Chemistry Gig 'em, Aggies! University of Cincinnati From owner-molec-model@net.bio.net Wed Jan 11 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!cornell!uw-beaver!netnews.nwnet.net!selway.umt.edu!not-for-mail From: samuelm@selway.umt.edu (Samuel J Mitchell) Newsgroups: bionet.software,bionet.molec-model Subject: Does a program exist for folding 23s rRNA ? Date: 10 Jan 1995 09:52:19 -0700 Organization: University of Montana, Missoula Lines: 15 Sender: samuelm@selway.umt.edu Message-ID: <3eue03$jl6@selway.umt.edu> NNTP-Posting-Host: selway.umt.edu Keywords: 23s, ribosome, folding program Xref: biosci bionet.software:10606 bionet.molec-model:229 Hello netters, We've recently stumbled into the gory world of 23s ribosomes, and are wondering if there are any programs (preferably public-domain) which can fold a 23s rRNA with some semblance of reality. I've checked the Ribosomal Database Project with no success, and we don't think that the PC-GENE RNAFOLD program (Zuker's algorithm) can handle such a long sequence. If anyone has any leads, or just tips on where we could get started on folding by hand, I'd really appreciate. Thanks in advance! Sam Mitchell samuelm@selway.umt.edu, (406) 243-5972 (Univ. of Montana) From owner-molec-model@net.bio.net Wed Jan 11 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!uunet!ankh.iia.org!babbage.ece.uc.edu!ucunix.san.uc.edu!ucunix.san.uc.edu!not-for-mail From: naussjl@ucunix.san.uc.edu (Jeffrey L Nauss) Newsgroups: bionet.molec-model Subject: InsightII and IRIX Date: 12 Jan 1995 09:00:11 -0500 Organization: University of Cincinnati Lines: 10 Message-ID: <3f3clb$n3v@ucunix.san.uc.edu> NNTP-Posting-Host: ucunix.san.uc.edu X-Newsreader: TIN [version 1.2 PL2] Has anyone else heard this rumour? With the next release of the Biosym software (current InsightII version is 2.3.5), IRIX 4.0.5 will no longer be supported. If true this means we will all have to upgrade to IRIX 5.3 if we still want to use Biosym products. -- Jeff Nauss Texas A&M Class of '77 Department of Chemistry Gig 'em, Aggies! University of Cincinnati From owner-molec-model@net.bio.net Thu Jan 12 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uxa.cso.uiuc.edu!dalke From: dalke@uxa.cso.uiuc.edu (Andrew Dalke) Newsgroups: bionet.molec-model Subject: NpT ensemble calculations Date: 13 Jan 1995 00:40:51 GMT Organization: University of Illinois at Urbana Lines: 28 Message-ID: <3f4i6j$re4@vixen.cso.uiuc.edu> NNTP-Posting-Host: uxa.cso.uiuc.edu We want to implement NpT ensemble calculations in our parallel MD code but are not sure how to do it. I looked at Berendsen's paper, and at the information in McCammon and Harvey, but the equations don't seem correct. Specifically, Berendsen's says: __ -> -> P=(2/3 V) ( E + 0.5 \ r . F ) k /_ ij ij i E is the kinetic energy , r is the vector from i to j k ij -> and F is the force on j from i ij Now, my problem is that this equation assumes there are only pair-wise forces, but we use the CHARMm parameter set; with angles, dihedrals, etc. These cannot be broken down into pair-wise forces, so the above equation doesn't work for MD. Am I correct? And if so, does anyone have a reference to a paper that tells how to include the higher body terms? Andrew Dalke dalke@ks.uiuc.edu From owner-molec-model@net.bio.net Thu Jan 12 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!xlink.net!rz.uni-karlsruhe.de!news.urz.uni-heidelberg.de!indi.oci.uni-heidelberg.de!stefan From: stefan@indi.oci.uni-heidelberg.de (Stefan Beyreuther) Newsgroups: bionet.molec-model Subject: SHELX .res files -> Insight II? Date: 12 Jan 1995 14:12:20 GMT Organization: University of Heidelberg, Germany Lines: 14 Distribution: world Message-ID: <3f3dc4$jcj@sun0.urz.uni-heidelberg.de> NNTP-Posting-Host: indi.oci.uni-heidelberg.de Keywords: SHELX, Insight II Who can import .res files generated by Sheldrick's X-ray software SHELXL-93 into Biosym's Insight II? Thanks Stefan _______________________________________________________________________________ Stefan Beyreuther Anorganisch-Chemisches Institut Tel 0049-6221-562565 Universitaet Heidelberg Fax 0049-6221-565707 69120 Heidelberg e-mail: stefan@indi.oci.uni-heidelberg.de Germany _______________________________________________________________________________ From owner-molec-model@net.bio.net Thu Jan 12 22:00:00 1995 Newsgroups: bionet.molec-model Path: biosci!agate!howland.reston.ans.net!swrinde!cs.utexas.edu!uunet!zib-berlin.de!gs.dfn.de!news.uni-bielefeld.de!ogretza From: ogretza@hrz.uni-bielefeld.de ( Olaf Gretza) Subject: thioredoxin Sender: news@hermes.hrz.uni-bielefeld.de (News Administrator) Message-ID: Date: Fri, 13 Jan 1995 14:26:05 GMT Nntp-Posting-Host: dave.hrz.uni-bielefeld.de Organization: Universitaet Bielefeld, Rechenzentrum X-Newsreader: TIN [version 1.2 PL2] Lines: 9 Hi folks, i am looking for a picture of thioredoxin. It would be nice if anyone could tell me where i can find one. It is for an homework, to be done until tuesday next week (as you can see i am in a hurry). If you know one, please tell me or leave a message here. Thanks. Olaf From owner-molec-model@net.bio.net Mon Jan 16 22:00:00 1995 Organization: harfang Subject: Conformational isomers and the brain Date: Tue, 17 Jan 95 00:36:41 -0500 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!swrinde!pipex!uunet!newsflash.concordia.ca!news.mcgill.ca!news.management.mcgill.ca!comback!harfang From: guy@harfang.login.qc.ca (Guy Tremblay) Newsgroups: bionet.molec-model Message-ID: <01-17-1995.44561@harfang> X-MKSIA-SN: 3990288132 Lines: 26 Hi! I read an article in the January '95 issue of Scientific American about PRIONS (proteinaceous infectious particle) disease. These new kinds of diseases are caused by conformational isomers of proteins present in the brain. These proteins, besides being pathogenic, are able to induce other proteins to adopt the same destructive conformation. I must say I was quite impressed by the discovery. I have a simple question: Is it possible that conformational isomers could be information storing systems for the brain? Is it possible that these isomers would have been unnoticed by researchers? There exists no "conformational isomers detectors"... yet. Is it possible that proteins could be the brain RAM ( or ROM...) or am I totally out of it? *************************************************************************** * Guy Tremblay Universite du Quebec a Montreal * * /\-/\ guy@harfang.login.qc.ca * * \\ ((O O)) // * * \\\ \\>// /// "But you musn't assume that a principle * * \\\\///\\//// that works at one level works at all levels" * * P.W. Anderson * *************************************************************************** From owner-molec-model@net.bio.net Tue Jan 17 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!uunet!world!news.bu.edu!nntp.bu.edu!rosenbac From: rosenbac@darwin.bu.edu (D. Srikar Rao) Newsgroups: bionet.molec-model Subject: pdb viewer Date: 18 Jan 1995 14:45:28 GMT Organization: Boston University Lines: 23 Distribution: world Message-ID: NNTP-Posting-Host: darwin.bu.edu Hi, I'm a graduate student working on protein modeling, and I'm trying to find out if there is some free software out there that allows for viewing pdb files on an XTERM. This software could be as simple as just allowing for rotation, but it would be nice if it allowed for only backbone, or alpha carbon trace, as well as allowed for picking individual atoms. Does such software exist for free out there? (something like Rasmol, but that would work on an xterm. If this isn't the place to post, can someone let me know where a good place to post would be? -- -- Dror Rosenbach Bio-molecular Engineering Research Center Off. (617) 353-7123 Dept. of Biomedical Engineering Res. (617) 776-6307 Boston University e-mail rosenbac@darwin.bu.edu There are three types of people in the world. Those that are good at math and those that are not. -- From owner-molec-model@net.bio.net Tue Jan 17 22:00:00 1995 Newsgroups: bionet.molec-model Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!cristal!lorenzo From: lorenzo@cristal (Gabriel Moreno Hagelsieb) Subject: InsightII vs. Quanta Message-ID: <1995Jan18.192455.4969@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: National Institutes of Health X-Newsreader: TIN [version 1.2 PL1] Date: Wed, 18 Jan 1995 19:24:55 GMT Lines: 16 Hi, Can anybody tell me how do Quanta and InsightII compare as to modeling of nucleic acids? Is Quanta really superior in this aspect? Thanks, Please e-mail your answers -- ________________________________________________________________ Lorenzo Segovia | IBT/UNAM | | Apdo. Postal 510-3 | lorenzo@pbr322.ceingebi.unam.mx | Col. Chamilpa 62210 | lorenzo@iris.ceingebi.unam.mx | Cuernavaca, Mor., Mexico | tel +(52)(73)11-49-00 to 04 | Fax +(52)(73)17-23-88 | ________________________________|_______________________________| From owner-molec-model@net.bio.net Wed Jan 18 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!pipex!uunet!zib-berlin.de!gs.dfn.de!news.gwdg.de!news From: heino.prinz@mpi-dortmund.mpg.de (Heino Prinz) Newsgroups: bionet.molec-model Subject: Re: Conformational isomers and the brain Date: 19 Jan 1995 14:46:51 GMT Organization: Max-Planck-Institut Dortmund Lines: 27 Message-ID: <3flu0r$b5i@gwdu19.gwdg.de> References: <01-17-1995.44561@harfang> NNTP-Posting-Host: m93213.mpi-dortmund.mpg.de X-Newsreader: WinVN 0.92.6+ In article <01-17-1995.44561@harfang>, guy@harfang.login.qc.ca (Guy Tremblay) says: > >Hi! > > I read an article in the January '95 issue of Scientific American >about PRIONS (proteinaceous infectious particle) disease. These new kinds >of diseases are caused by conformational isomers of proteins present in >the brain. These proteins, besides being pathogenic, are able to induce >other proteins to adopt the same destructive conformation. > I must say I was quite impressed by the discovery. I have a simple >question: Is it possible that conformational isomers could be information >storing systems for the brain? Is it possible that these isomers would >have been unnoticed by researchers? There exists no "conformational >isomers detectors"... yet. Is it possible that proteins could be the brain >RAM ( or ROM...) or am I totally out of it? > Yes, of course such a thing might be possible. But it would require a mechanism by which different isomers are formed or modulated in the process of developing long-term memory. I think that it is unlikely that such a mechanism has escaped detection so far. Still, I think it might be an exiting new area of research. In order to do it properly, one has to develop the tools of protein chemistry in these lipid- water interfaces. - Not an easy task! Heino From owner-molec-model@net.bio.net Wed Jan 18 22:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!hudson.lm.com!godot.cc.duq.edu!ddsw1!ns2.mainstreet.net!ablecom!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!max From: max@mycroft.mmid.ualberta.ca (Max Cummings) Newsgroups: bionet.molec-model Subject: Surface area calc's on `un-natural' molecules? Date: 19 Jan 1995 23:19:18 GMT Organization: it again! Lines: 14 Message-ID: <3fms1m$15e4@quartz.ucs.ualberta.ca> NNTP-Posting-Host: clouseau.mmid.ualberta.ca X-Newsreader: TIN [version 1.2 PL2] Hi, I am wondering about the availability of programs that calculate the surface areas of molecules which are not peptides or nucleic acids (ie programs which can deal with all kinds of drug0like small molecules). None of the programs i have encountered are set up to deal with this. Do you know of anything? Thanks, -- Max Cummings_____max@clouseau.mmid.ualberta.ca From owner-molec-model@net.bio.net Thu Jan 19 22:00:00 1995 Path: biosci!rutgers!csn!yuma!purdue!mozo.cc.purdue.edu!cv4.chem.purdue.edu!lev From: "Lev A. Gorenstein" Newsgroups: bionet.molec-model Subject: Re: pdb viewer Date: Fri, 20 Jan 1995 14:42:51 -0500 Organization: Purdue University Lines: 22 Message-ID: References: NNTP-Posting-Host: cv4.chem.purdue.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: On 18 Jan 1995, D. Srikar Rao wrote: > out if there is some free software out there that allows for viewing pdb > files on an XTERM. This software could be as simple as just allowing for > rotation, but it would be nice if it allowed for only backbone, or alpha > carbon trace, as well as allowed for picking individual atoms. Does such > software exist for free out there? (something like Rasmol, but that would > work on an xterm. Rasmol works very well on XTERM! We have it working on IBM RS/6000 AIXWindows. ftp to kekule.osc.edu and download it. Lev. ____________________________________________ Lev A. Gorenstein Chemistry Department Purdue University W.Lafayette, IN 47907, USA (317)494-9150; Fax (317)494-0239 lev@chem.purdue.edu From owner-molec-model@net.bio.net Sun Jan 22 22:00:00 1995 Newsgroups: bionet.molec-model Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uunet!world!chi From: chi@world.std.com (Cambridge Healthtech Institute) Subject: Computer-Aided Drug Development Meeting Message-ID: Organization: The World Public Access UNIX, Brookline, MA X-Newsreader: TIN [version 1.2 PL2] Date: Mon, 23 Jan 1995 21:20:41 GMT Lines: 22 Cambridge Healthtech Institute is sponsoring a conference on Computer-Aided Drug Development to be held on April 12-13, 1995 in San Francisco, CA. Computers have taken on an increasing role in drug development. They are being used for a wide range of tasks, from managing and analyzing data from high volume screening to the modeling and simulation requirements of structure-based drug development. Future prospects for data interpretation, visualization and molecular modeling will be highlighted. For more information contact Cambridge Healthtech Institute: chi@world.std.com. (Provide address & fax number for quick response). *********************************************************************** *>>>>>>>>>>>> Cambridge Healthtech Institute <<<<<<<<<<<<<* *>>>>> 1000 Winter Street, Suite 3700 <<<<<* *~~~~~~~~~~~~~~~~~ Waltham, MA 02154 ~~~~~~~~~~~~~~~~~* *tel: 617.487.7989 fax: 617.487.7937* *e-mail chi@world.std.com ++++++++ ftp: ftp.std.com: /pub/chi* *>>>>>>>>>>>>World Wide Web: http://id.wing.net/~chi/homepg.html<<<<<<* *********************************************************************** From owner-molec-model@net.bio.net Sun Jan 22 22:00:00 1995 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!helium.gas.uug.arizona.edu!bear From: bear@helium.gas.uug.arizona.edu (Soaring Bear) Newsgroups: bionet.molec-model Subject: Re: Conformational isomers and the brain Date: 23 Jan 1995 20:51:03 GMT Organization: University of Arizona, Unix Users Group Lines: 17 Message-ID: <3g14rn$2rm@news.CCIT.Arizona.EDU> References: <01-17-1995.44561@harfang> NNTP-Posting-Host: helium.gas.uug.arizona.edu In article <01-17-1995.44561@harfang>, Guy Tremblay wrote: > I read an article in the January '95 issue of Scientific American >about PRIONS (proteinaceous infectious particle) disease. These new kinds >...... I haven't read this article but the hypothesis of prions is hardly new. A small circle of people propounding this idea have been pushing it for at least a decade on tenuous grounds. -- ___ __ Listening may be the most (___ | .) important thing we do today! ___)OARING |__)ear, Cyber-Chemist UA New Pharmacy 404, Tucson AZ 85721 bear@ellington.pharm.arizona.edu From owner-molec-model@net.bio.net Mon Jan 23 22:00:00 1995 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!duke.usask.ca!switenky From: switenky@duke.usask.ca (Shawn Elliot Switenky) Newsgroups: bionet.molec-model,bionet.software Subject: HyperChem V2 Help with color printing Date: 24 Jan 1995 16:27:31 GMT Organization: University of Saskatchewan Lines: 27 Message-ID: <3g39pj$pkq@tribune.usask.ca> NNTP-Posting-Host: duke.usask.ca Summary: Need help with HyperChem Keywords: HyperChem AutoDesk Help Printing X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molec-model:242 bionet.software:10767 I'm having problems getting HyperChem Version 2 working with a color printer. They have a 486 8 Meg machine running Windows and HyperChem. They would like to print using their HP DeskJet 560C printer. The HP printer driver is installed, and HyperChem is using it. The problem involves color output. I cannot make the output in color no matter what I do. I can make the printer print in color from other applications. I can cut a image of the HyperChem window, paste it into another application and print it in color that way. Of course, cut and paste restricts the image to screen resolution, and the printer can provide much higher resolution in black&white from HyperChem. But I can't get HyperChem to print in color on this printer. If anyone knows how to print in color using HyperChem, please let me know. If HyperChem cannot print in color, I'd like to know that as well. Thanks for your help! -- + Shawn Switenky --------------+ email: Shawn.Switenky@USask.CA ---+ ///| User Support | Phone: (306) 966-4983 | /// | Computing Services | Fax: (306) 966-4938 | \\\/// + University of Saskatchewan --+ ICBM: N52 07'53.1" W106 37' 57.9" + \XX/ | At Intel, Quality is Job 0.999897256. | +------------------------------------------------------------------+ From owner-molec-model@net.bio.net Tue Jan 24 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!news.oleane.net!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!newsfeed.ACO.net!aci.cvut.cz!sun.uakom.sk!sun.uakom.sk!not-for-mail From: kurz3@sun.uakom.sk (kurz 3) Newsgroups: bionet.molec-model Subject: Re: Conformational isomers and the brain Date: 24 Jan 1995 16:30:27 +0100 Organization: UAKOM Banska Bystrica Lines: 33 Distribution: world Message-ID: <3g36ej$kkk@sun.uakom.sk> References: <01-17-1995.44561@harfang> NNTP-Posting-Host: sun.uakom.sk X-Newsreader: TIN [version 1.2 PL2] Guy Tremblay (guy@harfang.login.qc.ca) wrote: : Hi! : I read an article in the January '95 issue of Scientific American : about PRIONS (proteinaceous infectious particle) disease. These new kinds : of diseases are caused by conformational isomers of proteins present in : the brain. These proteins, besides being pathogenic, are able to induce : other proteins to adopt the same destructive conformation. : I must say I was quite impressed by the discovery. I have a simple : question: Is it possible that conformational isomers could be information : storing systems for the brain? Is it possible that these isomers would : have been unnoticed by researchers? There exists no "conformational : isomers detectors"... yet. Is it possible that proteins could be the brain : RAM ( or ROM...) or am I totally out of it? : *************************************************************************** : * Guy Tremblay Universite du Quebec a Montreal * : * /\-/\ guy@harfang.login.qc.ca * : * \\ ((O O)) // * : * \\\ \\>// /// "But you musn't assume that a principle * : * \\\\///\\//// that works at one level works at all levels" * : * P.W. Anderson * : *************************************************************************** Prions is closely related with chaperons. One of their main tasks is transport of the some proteins across the cytoplasmatic membrane and repair of damaged structure of proteins. Chaperons are enable to unfold and fold proteins, which was structuraly damaged f.e. in the stress conditions. In my opinion it is may be other function of this proteins From owner-molec-model@net.bio.net Wed Jan 25 22:00:00 1995 Path: biosci!rutgers!uwm.edu!caen!newsxfer.itd.umich.edu!agate!news.ucdavis.edu!library.ucla.edu!news.mic.ucla.edu!hodgkin.mbi.ucla.edu!arne From: arne@hodgkin.mbi.ucla.edu (Arne Elofsson) Newsgroups: bionet.molec-model Subject: Re: Conformational isomers and the brain Date: 26 Jan 1995 00:00:09 GMT Organization: OrgFreeware Lines: 30 Distribution: world Message-ID: <3g6om9$ke9@news.mic.ucla.edu> References: <01-17-1995.44561@harfang> <3g36ej$kkk@sun.uakom.sk> Reply-To: arne@hodgkin.mbi.ucla.edu (Arne Elofsson) NNTP-Posting-Host: hodgkin.mbi.ucla.edu P.W. Anderson writes> :Prions is closely related with chaperons. One of their main tasks is :transport of the some proteins across the cytoplasmatic membrane and repair :of damaged structure of proteins. Chaperons are enable to unfold and fold :proteins, which was structuraly damaged f.e. in the stress conditions. : In my opinion it is may be other function of this proteins This is wrong, Prions are not closely related to chaperones. Chaperones might be involved in prions diseases, but chaparones helps protein to fold and prions are wrongly folded proteins. It is a big difference -- ****************************************************************************** ** From: Arne Elofsson ** ** Fax: +1-(310)-206-3914 or Fax: +1-(310)-206-7286 ** ** Tel: +1-(310)-825-1402 ** ** ** ** Email: arne@hodgkin.mbi.ucla.edu (arne@uclaue.mbi.ucla.edu) ** ** ** ** WWW: http://www.doe-mbi.ucla.edu/arne/main.html ** ** WWW: http://www.mbi.ucla.edu/arne/main.html ** ** ** ** Adress: Molecular Biology Institute Home: 1370 Veteran #311 ** ** 405 Hilgard Avenue, UCLA Los Angeles ** ** Los Angeles CA 90024 ** ** California 90095 USA ** ** USA Tel: +1-(310)-268-8006 ** ****************************************************************************** From owner-molec-model@net.bio.net Wed Jan 25 22:00:00 1995 Newsgroups: bionet.molec-model Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!helix.nih.gov!smohan From: Mohan Srinivasan Subject: DOES GRAVITY AFFECT PROTEIN FOLDING ? Content-Type: TEXT/PLAIN; charset=US-ASCII Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Cc: Mohan Srinivasan Organization: National Institutes of Health Mime-Version: 1.0 Date: Thu, 26 Jan 1995 22:53:19 GMT Lines: 17 Hi All- Can proteins fold in a different way in the absence of gravity ? I believe that their density changes (compacts) when spun in ultracentrifuges at high rpm's (high G). So, the reverse (low G) should be also true. Gravity is one of the forces apart from the nuclear forces. Does folding depend only on nuclear forces ? I am not sure though. Was any study made in this direction during space experiments ? Could anyone throw some light ? Mohan Srinivasan Ph.D | email: smohan@helix.nih.gov DCBDC/NCI/Bldg 37 Rm 2B10,NIH,9000 Rockville Pike| phone: 301 496 2202 Bethesda, MD 20892, USA | fax : 301 402 1031 From owner-molec-model@net.bio.net Thu Jan 26 22:00:00 1995 Newsgroups: bionet.molec-model Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!rvenable From: rvenable@deimos.cber.nih.gov (Rick Venable) Subject: Re: DOES GRAVITY AFFECT PROTEIN FOLDING ? Message-ID: <1995Jan27.024118.3087@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: FDA/CBER Biophysics Lab X-Newsreader: TIN [version 1.2 PL2] References: Date: Fri, 27 Jan 1995 02:41:18 GMT Lines: 36 On Thu, 26 Jan 1995 22:53:19 GMT Mohan Srinivasan pontificated: > Can proteins fold in a different way in the absence of > gravity ? I believe that their density changes (compacts) when > spun in ultracentrifuges at high rpm's (high G). So, the reverse > (low G) should be also true. Gravity is one of the forces apart > from the nuclear forces. Does folding depend only on nuclear > forces ? I am not sure though. Was any study made in this direction > during space experiments ? Could anyone throw some light ? I'd say that there is little or no difference. First, the difference between 0 G and 1 G is very small, compared to the high G force in a modern ultracentrifuge. Second, perhaps many astronauts would be dead if the change from 1 G to 0 G seriously altered protein folding. Third, most theoretical chemistry programs (molecular dynamics, quantum calculations, etc.) ignore gravity completely. Not that the absence is proof, but many leading scientists studying protein folding from a theoretical approach do not consider gravity. After all, the mass of a protein is infintesimal compared to the mass of the Earth, and it exists in a buoyant medium. Folding does not depend on nuclear forces, but electrostatic forces (charge attraction and repulsion) and the mostly attractive London dispersion, or van der Waals, forces. The charge interactions can be fairly long range, easily 2-5 times the zero point as van der Waals forces; the latter forces are close to zero for atom interactions further than 10 Angstroms apart. Finally, I'm sure there have been 0 G protein crystallization experiments on the space shuttle, as well as a fair number of biochemistry and biological experiments. Perhaps they've even made blood density measurements. NASA is very foward about providing access to the results of their work, both as publications and on-line thru gopher and www servers. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| / Not an official statement \ rvenable@deimos.cber.nih.gov \/ |=| \ or position of the FDA. / From owner-molec-model@net.bio.net Thu Jan 26 22:00:00 1995 Newsgroups: bionet.molec-model Path: biosci!newshost.lanl.gov!news.ttu.edu!aurora.LaTech.edu!darwin.sura.net!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Re: DOES GRAVITY AFFECT PROTEIN FOLDING ? Message-ID: <1995Jan27.163228.18517@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health References: Date: Fri, 27 Jan 1995 16:32:28 GMT Lines: 49 In article , Mohan Srinivasan writes: |> |> Hi All- |> |> Can proteins fold in a different way in the absence of |> gravity ? I believe that their density changes (compacts) when |> spun in ultracentrifuges at high rpm's (high G). So, the reverse |> (low G) should be also true. Gravity is one of the forces apart |> from the nuclear forces. Does folding depend only on nuclear |> forces ? I am not sure though. Was any study made in this direction |> during space experiments ? Could anyone throw some light ? |> |> Mohan Srinivasan Ph.D | email: smohan@helix.nih.gov |> DCBDC/NCI/Bldg 37 Rm 2B10,NIH,9000 Rockville Pike| phone: 301 496 2202 |> Bethesda, MD 20892, USA | fax : 301 402 1031 |> |> |> Just to add yet another NIH voice to this-- The magnitude of gravitational forces is extremely small compared to the magnitude of electrostatic forces. That's why a kitchen magnet can hold a note to the fridge with the entire gravitational force of the Earth pulling against it. Of course, electrostatics (salt bridges, Hbonds, vdW, etc.) do not determine folding by themselves--entropic considerations are nearly equal. The free energy of stabilization of most folded proteins' structure is typically 20 kcal/mol at 25C, but the aggregate size of the electrostatic forces holding the folded structure together is on the order of thousands of kcal/mol. Entropy nearly balances electrostatics. And yes, some protein crystals have been grown on the Shuttle, but they're usually so fragile that they're unusable. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| From owner-molec-model@net.bio.net Sun Jan 29 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uunet!comp.vuw.ac.nz!canterbury.ac.nz!chmeds.ac.nz!gjacobs From: gjacobs@chmeds.ac.nz Newsgroups: bionet.molec-model Subject: Re: DOES GRAVITY AFFECT PROTEIN FOLDING ? Message-ID: <1995Jan31.092552.868@chmeds.ac.nz> Date: 31 Jan 95 09:25:52 +1200 References: <1995Jan27.024118.3087@alw.nih.gov> Lines: 33 (just in fun - this is not really my topic!) In article <1995Jan27.024118.3087@alw.nih.gov>, rvenable@deimos.cber.nih.gov (Rick Venable) writes: > On Thu, 26 Jan 1995 22:53:19 GMT Mohan Srinivasan pontificated: >> Can proteins fold in a different way in the absence of >> gravity ? I believe that their density changes (compacts) when >> spun in ultracentrifuges at high rpm's (high G). So, the reverse >> (low G) should be also true. Gravity is one of the forces apart >> from the nuclear forces. Does folding depend only on nuclear >> forces ? I am not sure though. Was any study made in this direction >> during space experiments ? Could anyone throw some light ? > > I'd say that there is little or no difference. First, the difference > between 0 G and 1 G is very small, compared to the high G force in a > modern ultracentrifuge. Second, perhaps many astronauts would be dead if > the change from 1 G to 0 G seriously altered protein folding. Nicely put. > Third, most > theoretical chemistry programs (molecular dynamics, quantum calculations, > etc.) ignore gravity completely. Not that the absence is proof, but many > leading scientists studying protein folding from a theoretical approach do > not consider gravity. After all, the mass of a protein is infintesimal > compared to the mass of the Earth, and it exists in a buoyant medium. > [snip] Just another thought - do proteins care "which way up" they are while they are folding - I doubt it! (a grativational effect implies a directional effect). Grant. From owner-molec-model@net.bio.net Sun Jan 29 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!howland.reston.ans.net!spool.mu.edu!caen!msunews!netnews.upenn.edu!wal6000a.udc.upenn.edu!lfmuscar From: lfmuscar@udcemail.udc.upenn.edu (Lawrence F. Muscarella) Newsgroups: bionet.molec-model Subject: PhD bioengineer seeks career change Date: 30 Jan 1995 22:41:56 GMT Organization: University of Pennsylvania Lines: 6 Message-ID: <3gjpvk$lf9@netnews.upenn.edu> NNTP-Posting-Host: wal6000a.udc.upenn.edu X-Newsreader: TIN [version 1.2 PL2] PhD bioengineer with experience in mathematical modeling of physiologic processes seeks employment in the field of molecular biology. Please send E-mail if you know of a position. -- lfmuscar@udcemail.udc.upenn.edu From owner-molec-model@net.bio.net Mon Jan 30 22:00:00 1995 Path: biosci!RON.F.U-TOKYO.AC.JP!shiota From: shiota@RON.F.U-TOKYO.AC.JP (SHIOTA Takeshi) Newsgroups: bionet.molec-model Subject: (none) Date: 30 Jan 1995 20:51:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <199501310451.NAA16089@ron.f.u-tokyo.ac.jp> NNTP-Posting-Host: net.bio.net Help ********************* shiota@ron.f.u-tokyo.ac.jp (Takeshi Shiota) ********************* From owner-molec-model@net.bio.net Mon Jan 30 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!gs.dfn.de!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!inherit.lmb.uni-muenchen.de!user From: steipe@lmb.uni-muenchen.de (Boris Steipe) Newsgroups: bionet.molec-model Subject: Re: DOES GRAVITY AFFECT PROTEIN FOLDING ? Followup-To: bionet.molec-model Date: 30 Jan 1995 11:42:29 GMT Organization: Genzentrum, biostructure lab Lines: 35 Distribution: world Message-ID: References: NNTP-Posting-Host: 141.84.48.171 In article , Mohan Srinivasan wrote: > Can proteins fold in a different way in the absence of > gravity ? The conformational free energy of a protein is primarily determined by electrostatic forces and entropy. These forces, on a molecular scale are _many_ orders of magnitude larger than the gravitational forces involved. Even more important, the possible perturbations due to gravitation are again _many_ orders of magnitude smaller than thermal perturbations under physiological conditions. We do not expect gravity to have noticable effetcs on protein folding. Even more so, since external applied fields homogeneously affect all atoms in the molecule, there is no gradient which might generate a force. On the other hand, gravity can affect protein concentration. Concentration affects the propensity towards aggregation and this influences unproductive side-reactions along the folding pathway. This is a question of kinetics, not thermodynamics. Protein crystallization has _many_ variables. The presence or absence of gravitational fields is one of them. It has been argued, that under microgravitational conditions, the absence of convective currents in the crystalization experiment should produce better crystals. Indeed, space-shuttle experiments have grown crystals, that are no worse than those which have been grown on earth ;-). But the reverse also works. A BioTechnology cover page some years ago showed crystals grown in the centrifuge, apparently high-G conditions favored nucleation under certain conditions. Greetings -- Boris From owner-molec-model@net.bio.net Tue Jan 31 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!EU.net!ub4b!idefix.CS.kuleuven.ac.be!news.fundp.ac.be!Newsmaster From: Isabelle.Reginster@fundp.ac.be (Isabelle Reginster) Newsgroups: bionet.molec-model Subject: molecular graphics softwares Date: 1 Feb 1995 10:13:53 GMT Organization: F.U.N.D.P. Biologie Quantitative Lines: 12 Sender: regin@lysine.biq.fundp.ac.be Message-ID: <3gnmt1$bci@hermes.fundp.ac.be> NNTP-Posting-Host: biq-mac1.biq.fundp.ac.be X-Posted-From: InterNews 1.0.4@biq-mac1.biq.fundp.ac.be X-Authenticated: regin on POP host lysine.biq.fundp.ac.be Hello, I'm searching for molecular graphics softwares, mostly for PC, but also for Mac, SGI and unix machines. Send your answers to regin@biq.fundp.ac.be I'll send a summary on this list. Thank you Isabelle Reginster Facultes Universitaires Notre Dame de la Paix, NAMUR, BELGIUM