From owner-molec-model@net.bio.net Fri Jan 02 22:00:00 1998 Path: biosci!CPCUG.ORG!winfield From: winfield@CPCUG.ORG Newsgroups: bionet.molec-model Subject: cops are on the way pinhead Date: 3 Jan 1998 06:22:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801031421.JAA26564@cpcug.org> NNTP-Posting-Host: net.bio.net thot you might want to know, i have alerted ATT card services and Worldnet about your pitiful scam cheers and have an unhappy new year At 02:58 AM 1/2/98 -0800, hell@hell.com wrote: >X-Newsreader: SgK9MsHtZEcuZIUQ > > >Ok, you can get money posted to your Visa, mastercard, or directly into your bank account by going the the following web address. When you go there you will see a line on the new user sign--up that says "if a friend sent you, put their e-mail address here" Now if you put this e-mail address (Insanity1@worldnet.att.net)there, we BOTH will get a dollar bonus. So go to http://cybergold.com and REMEMBER USE this E-mail address under the Who referred you? section: "Insanity1@worldnet.att.net" > >----------------------------------------------------- >Broaden your exposure on the Internet >Get your free trial Bulk Email strip/send software >Send requests to: mf_mf@hotmail.com > > > From owner-molec-model@net.bio.net Tue Jan 06 22:00:00 1998 Newsgroups: bionet.molec-model Path: biosci!agate!logbridge.uoregon.edu!sunqbc.risq.qc.ca!nntp.texas.net!uunet!in1.uu.net!world!wware-nospam From: wware-nospam@world.std.com (Will Ware) Subject: PSF file format Message-ID: Organization: The World Public Access UNIX, Brookline, MA X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 7 Jan 1998 14:07:41 GMT Lines: 47 I have been starting to get acquainted with the NAMD modeling package, and I hope somebody patient will be willing to answer what are probably some very basic questions. I see that in the sample data for NAMD, there are four files (alanin (a NAMD script), alanin.pdb, alanin.params, and alanin.psf). I am clear on the first three files, and I can understand most of what's going on with the psf file, but there are a few things in it that I don't understand. Here is a short segment of it: 66 !NATOM 1 MAIN 1 ACE CA CH3E 0.000000E+00 15.0350 0 2 MAIN 1 ACE C C 0.450000 12.0110 0 3 MAIN 1 ACE O O -0.450000 15.9994 0 4 MAIN 2 ALA N NH1 -0.350000 14.0067 0 5 MAIN 2 ALA H H 0.250000 1.00800 0 6 MAIN 2 ALA CA CH1E 0.100000 13.0190 0 7 MAIN 2 ALA CB CH3E 0.000000E+00 15.0350 0 etcetera It's clear that the numbers over here ---------------/\ are masses, and I can see that the CA and CB notations are used to represent small clumps of carbons and hydrogens. What are ----/\ these numbers? My best guess is that they are fractional electric charges due to electron imbalances in covalent bonds, have I got that right? And if so, would I be correct in guessing that they are fractions of a proton charge? Later in the file, there are a couple of sections for "donors" and "acceptors". I'm guessing this is probably a really dumb question, but what is being donated and accepted? Donors always seem to be hydrogens and nitrogens, and acceptors seem to be lone carbons and oxygens. I've done a little reading about molecular mechanics modeling and I'm not clear what acceptors and donors are in this context, and how they are involved with modeled interatomic forces. My last question is, where does the PSF file come from? It looks like it is derived from the PDB file. I can imagine a program that reads in the PDB file, figures out bonds based on interatomic distances, and then enumerates which bond, angle, dihedral, and improper energy terms are needed to model it, along with the other stuff in the file. If that's the case, where do I find the software to generate the PSF file? It doesn't seem to have come with the NAMD program. Thanks for any answers anybody can provide for these questions. -- ------------------------------------------------------------- People say that everyone has a few skeletons in their closet. Not me. Well, not yet anyway. I mean, the bodies are still decomposing. Will Ware email: wware[at]world[dot]std[dot]com From owner-molec-model@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!ais.net!uunet!in1.uu.net!iafrica.com!uct.uni.net.za!csir.uni.net.za!news.up.ac.za!biomac.up.ac.za!user From: fourie@scientia.up.ac.za (Fourie Joubert) Newsgroups: bionet.molec-model,bionet.software Subject: sybdb script in DOCK? Date: Thu, 08 Jan 1998 13:06:12 +0200 Organization: University of Pretoria Lines: 9 Message-ID: NNTP-Posting-Host: biomac.up.ac.za Xref: biosci bionet.molec-model:1977 bionet.software:20277 Hi Does anyone know of an update for the sybdb script in DOCK4.0 that works with Sybyl 6.2 or 6.3's SPL? Thanks! Fourie Joubert fourie@scientia.up.ac.za From owner-molec-model@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!newsxfer3.itd.umich.edu!newsxfer.itd.umich.edu!sunqbc.risq.qc.ca!peerfeed.ncal.verio.net!nntp2.cerf.net!nntp3.cerf.net!ihnp4.ucsd.edu!news.scripps.edu!not-for-mail From: Don Bashford Newsgroups: bionet.molec-model Subject: Re: PSF file format Date: 08 Jan 1998 13:43:59 -0800 Organization: The Scripps Research Institute, La Jolla, CA, USA Lines: 40 Message-ID: References: NNTP-Posting-Host: gage.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Gnus v5.5/Emacs 20.2 I'm more of a CHARMM person than a NAMD person, but these two programs have the PSF in common, so I can answer your questions. You are correct about the electric charges, as well as the other guesses you made about the PSF snippet you posted. "Donors" and "acceptors" refer to hydrogen bonds. Some of the older molecular mechanics empirical functions used explicit H-bonding terms, but in the 80s there was a move toward dropping these in favor charges and van der Waals terms with parameters tuned to reproduce H-bonding effects. Even so, many molecular mechanics programs retain the capability of explicit hydrogen bonding for purposes like counting up H-bonds. PSF stands for Protein Structure File. You seem to be pretty clear about the sort of information it contains, so I won't explain that, but your guess about how it is generated is probably not correct. The CHARMM program (from the Karplus group at Harvard Chem. Dept.) generates a PSF after first reading a Residue Topology File (RTF) and then the protein sequence. The RTF has bond-connectivity and charge information for all the amino-acid residue types, as well as information about how conntectivity and so forth change when you link them together into a peptide chain or make other covalent modifications like a Cys-Cys crosslink or protonation of a carboxylate. This information, in combination with the desired residue sequence, and perhaps some directives to make other covalent modifications, is sufficient to allow construction of the PSF without reading any coordinates. The X-PLOR program (from Axel Brunger of Yale) which is closely related to CHARMM also generates PSF files, but in a slightly different format than CHARMM. Some molecular mechanics programs don't generate their own PSFs because it is a complicated thing to program. Instead, they rely on a program like CHARMM or X-PLOR to do it for them. I don't know whether NAMD is one of these, but I think that some of the older programs from the Schulten group (NAMD's origin) did use externally generated PSFs. Donald Bashford The Scripps Research Institute From owner-molec-model@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!206.246.194.8!newsxfer.visi.net!nntp.texas.net!nntp.flash.net!news.mira.net.au!harbinger.cc.monash.edu.au!newshost.carno.net.au!torda From: Andrew.Torda@anu.edu.au Newsgroups: bionet.molec-model,bionet.info-theory Subject: Post-doc in computational chemistry, Canberra, Australia with Andrew Torda Date: 9 Jan 1998 05:58:21 GMT Organization: Research School of Chemistry, Australian National University Lines: 69 Sender: Andrew.Torda@anu.edu.au Message-ID: <694e9t$ddk$1@clarion.carno.net.au> Reply-To: Andrew.Torda@anu.edu.au NNTP-Posting-Host: 150.203.35.129 Originator: torda@rsc.anu.edu.au Xref: biosci bionet.molec-model:1979 bionet.info-theory:5996 POST DOCTORAL POSITION Computational Chemistry in The Research School of Chemistry, Canberra, Australia with Andrew Torda Available immediately. 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, mixing knowledge-based force fields with experimental data and combinatorial algorithms for protein sequence optimisation. All the projects in the group involve coding and development - 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). Possible projects would be centred around some new algorithms for aligning amino acid sequences to structures, based on the force fields we have developed. These might include some entertaining ideas such as quasi-Newtonian dynamics in amusing spaces. Projects are negotiable. Salary: more than $40,963 - $43,834 per annum (the rates just increased a week ago). Grants are provided towards travel and removal. Positions are initially for two years with a possible extension to a third year. 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. There are no 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, polymer theory, 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. Anyone interested in the Torda group should look at http://www.rsc.anu.edu.au/~torda That also contains a pointer to a page of recent publications. Anyone interested should contact me directly (Andrew.Torda@anu.edu.au). The closing date for applications will be March 3 1998. The administrative procedure is that, if you are interested, you are sent an official application (by slow mail). Applicants then have to fill this out and mail it back (again by slow mail). The official forms will include a request for comments from three referees. There is an old advertisement from a previous school-wide job offer at http://www.rsc.anu.edu.au/RSC/AcademicPositions/RSC_Academic_Positions.html and read under "Postdoctoral Fellowships". Andrew Torda From owner-molec-model@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!ais.net!vixen.cso.uiuc.edu!ks.uiuc.edu!dalke From: dalke@ks.uiuc.edu (Andrew Dalke) Newsgroups: bionet.molec-model Subject: Re: PSF file format Date: 11 Jan 1998 09:19:05 GMT Organization: TB BI Lines: 33 Distribution: world Message-ID: <69a2q9$80h$1@vixen.cso.uiuc.edu> References: NNTP-Posting-Host: ophelia.ks.uiuc.edu Don Bashford pretty much explained everything, but I want to fill in some minor details. The PSF file used by NAMD comes from XPLOR, which is a variation of the PSF format of CHARMM's. The NAMD developers (of which I was one) decided to leave the complications to XPLOR, because it is a hard problem. We chose XPLOR because that's what we had in-house. Will Ware asked how to generate a PSF file. The only way I can suggest to do it is get a copy of XPLOR (or of CHARMM and write a conversion script; it is a pretty simple translation). This isn't a satisfactory answer, but I know of no freely available program that will do this. Hint to anyone reading this; many people would thank you if you wrote one! We were not able to find a good description of the PSF format; we had to discover it from reverse engineering. I still don't know what the last column of the ATOM line describes: 66 !NATOM 1 MAIN 1 ACE CA CH3E 0.000000E+00 15.0350 0 This one ---^ Will also asked a few questions about the h-bond donor/acceptor lines. For NAMD, those are ignored because the CHARMM force field no longer depends on it. Plus, reverse engineering that section of the code was nasty. Andrew dalke@mag.com --- Not speaking for the Molecular Applications Group. From owner-molec-model@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!newsrelay.netins.net!nntp.kreonet.re.kr!xfer.kren.nm.kr!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!atl.bellsouth.net!news4.atl.bellsouth.net.POSTED!not-for-mail From: isp@fcc.gov (concerned user) Newsgroups: bionet.molec-model Subject: test Message-ID: <34ba4810.3316420@news.atl.bellsouth.net> X-Newsreader: Forte Agent 1.5/32.452 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 1 Date: Sun, 11 Jan 1998 22:30:34 GMT NNTP-Posting-Host: host-209-138-17-170.atl.bellsouth.net NNTP-Posting-Date: Sun, 11 Jan 1998 17:30:34 EST From owner-molec-model@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.125.85.9!news.mv.net!newspump.wustl.edu!newsreader.wustl.edu!not-for-mail From: reece@whoville.wustl.edu Newsgroups: bionet.molec-model Subject: RASMOL: linux patch for 2.6beta Date: 12 Jan 1998 08:40:12 -0600 Organization: Biophysics & Biochemistry, Washington University, St. Louis, USA Lines: 32 Message-ID: <82k9c5oiwj.fsf@whoville.wustl.edu> Reply-To: Reece Kimball Hart NNTP-Posting-Host: whoville.wustl.edu X-Attribution: Reece X-URL: X-Newsreader: Gnus v5.5/Emacs 20.2 -----BEGIN PGP SIGNED MESSAGE----- This patch is for RasMol 2.6beta on linux systems. It has no effect in other environments. It corrects the following compilation errors: rasmol.c: In function `FetchCharacter': rasmol.c:491: `WaitSet' has an incomplete type rasmol.c:497: warning: passing arg 2 of `select' ... rasmol.c:497: warning: passing arg 3 of `select' ... rasmol.c:497: warning: passing arg 4 of `select' ... rasmol.c: At top level: rasmol.c:112: storage size of `OrigWaitSet' isn't known rasmol.c:113: storage size of `WaitSet' isn't known The patch is available at http://dasher.wustl.edu/~reece/src/RasMol2.6b-linux-01.patch.gz ftp://dasher.wustl.edu/pub/reece/src/RasMol2.6b-linux-01.patch.gz - -- Reece Hart, http://dasher.wustl.edu/~reece/ Do not send unsolicited bulk email. Boycott companies which do so. -----BEGIN PGP SIGNATURE----- Version: 2.6.3ia Charset: noconv Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface iQCVAwUBNLlMskxUVHHReKr5AQGydgP9HK/GGm9A28jYbN5fDk6Ox/WWuF5UO/Ce rUrZYPgcYcmWjkl9zQMUfErYOSlCN+Vnj1M+qtyBKCU1ji88Qs9Hy1bh339E9+HF s2837ySCToPw+la/3Yp8btwcVUI48BtPdIXPgrXnqqH5yh9t1EvmOWji/XbmVI1y 6OGEwtLB23Y= =n8kW -----END PGP SIGNATURE----- From owner-molec-model@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.125.85.9!news.mv.net!newspump.wustl.edu!newsreader.wustl.edu!not-for-mail From: reece@whoville.wustl.edu Newsgroups: bionet.molec-model Subject: RASMOL: spaceorb patch for 2.6beta Date: 12 Jan 1998 08:41:18 -0600 Organization: Biophysics & Biochemistry, Washington University, St. Louis, USA Lines: 29 Message-ID: <82iurpoiup.fsf@whoville.wustl.edu> Reply-To: Reece Kimball Hart NNTP-Posting-Host: whoville.wustl.edu X-Attribution: Reece X-URL: X-Newsreader: Gnus v5.5/Emacs 20.2 -----BEGIN PGP SIGNED MESSAGE----- This patch adds SpaceOrb360 support to RasMol 2.6beta. This patch has only been tested with Linux; compatibility reports and patches for other systems are appreciated. The SpaceOrb is a 6 degree of freedom joystick. It looks like a baseball mounted on a short shaft; the baseball rotates ±20° or so and translates about ±5mm from rest. See http://www.spaceorb.com. Thanks to John Stone for orb.[ch]. The patch is available at http://dasher.wustl.edu/~reece/src/RasMol2.6b-spaceorb-01.patch.gz ftp://dasher.wustl.edu/pub/reece/src/RasMol2.6b-spaceorb-01.patch.gz - -- Reece Hart, http://dasher.wustl.edu/~reece/ -----BEGIN PGP SIGNATURE----- Version: 2.6.3ia Charset: noconv Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface iQCVAwUBNLlS1UxUVHHReKr5AQGfIgP/dr+SRTsRWAakjP1so8BmxoeWK3gTBVGQ gWU9fRiCYz1lE/lLVExULQOfRN34vSQt3nGp2OkrAbAr645xAP89qJiD82QeY5SH dCs3EwcSmJtYffxz1yGVXxdKSLizcEA9fM7QuMweRta8c1WnnrtPReub82PnZ2tM 22HTQqbelKw= =Al3k -----END PGP SIGNATURE----- From owner-molec-model@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!REMOVE.THIS.techfak.uni-bielefeld.de!fuellen From: fuellen@REMOVE.THIS.techfak.uni-bielefeld.de (Georg Fuellen) Newsgroups: bionet.molec-model Subject: Distance Training in the Biosciences, a 5-minute Questionaire Date: 12 Jan 1998 15:11:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801122311.AAA26694@salbei.TechFak.Uni-Bielefeld.DE> Reply-To: fuellen@TechFak.Uni-Bielefeld.DE NNTP-Posting-Host: net.bio.net (apologies for crossposting) Dear Madam or Sir, Biology and medicine as of today demand more and more skills in Bioinformatics. Since University curricula do not yet satisfy this need, a group of Bioinformatics researchers at the University of Bielefeld plans to establish a training program filling this gap. The planned courses consist of modules designed and conducted by distinguished researchers and lecturers. Each module covers a special topic and spans one month, each week including 4 hours self-study of hypertext material and 2 hours discussion with a lecturer in a 'virtual classroom' or in your company or academic institution. We would like to ask you to complete the questionnaire at http://oleander.TechFak.Uni-Bielefeld.DE:8080/cgi-bin/e2 to help us evaluate the actual demand. Thank you for your help ! Yours faithfully, The DisTrain planning commitee. Christian Bueschking Georg Fuellen Chris Schleiermacher Alexander Sczyrba Prof. Robert Giegerich (academic advisor) ======== P.S. We hope to sustain our free offerings (on an entry level, like the VSNS Biocomputing Courses we did in 1995 and 1996, see http://www.techfak.uni-bielefeld.de/bcd/welcome.html) by offering more advanced courses for a fee. If you're interested in future offerings, please visit http://www.techfak.uni-bielefeld.de/bcd/plans.html. From owner-molec-model@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!MS.CC.NTU.EDU.TW!r5447003 From: r5447003@MS.CC.NTU.EDU.TW (Ling) Newsgroups: bionet.molec-model Subject: Cavity Volume of Enzyme Active Site Date: 13 Jan 1998 01:49:14 -0800 Organization: Institute of Biomedical Sciences, Acadmia Sinica Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <349337B6.167E@ms.cc.ntu.edu.tw> NNTP-Posting-Host: net.bio.net Dear Netters: I am studying an enzyme with a gorge-like active site, which can be bound by substrates or inhibitors. Can anyone suggest programs to measure the volume of cavity ? Any suggestions are appreciated. Y. L. Luo From owner-molec-model@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!howland.erols.net!surfnet.nl!ruu.nl!not-for-mail From: "Jurgen F. Doreleijers" Newsgroups: bionet.molec-model Subject: Re: Cavity Volume of Enzyme Active Site Date: Wed, 14 Jan 1998 11:28:58 +0000 Organization: NMR spectroscopy; Utrecht University; The Netherlands Lines: 11 Message-ID: <34BCA17A.41C6@nmr.chem.ruu.nl> References: <349337B6.167E@ms.cc.ntu.edu.tw> NNTP-Posting-Host: mule.chem.ruu.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP22) To: Ling Try: http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html http://www.sander.embl-heidelberg.de/whatif/chap31.html Hope it helps, Jurgen -- Drs Jurgen F. Doreleijers NMR spectroscopy, Utrecht University, The Netherlands mailto:jurgen@nmr.chem.ruu.nl http://www-nmr.chem.ruu.nl/users/jurgen/jurgen.html From owner-molec-model@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!141.211.144.13!newsxfer3.itd.umich.edu!news.eecs.umich.edu!newshub.tc.umn.edu!newsstand.tc.umn.edu!usenet From: "Alan J. Robinson" Newsgroups: bionet.molec-model Subject: Protein Folding Date: Wed, 14 Jan 98 07:27:42 CST Organization: University of Minnesota Lines: 21 Message-ID: <41125.robin073@tc.umn.edu> NNTP-Posting-Host: pub-18-c-167.dialup.umn.edu X-Minuet-Version: Minuet1.0_Beta_18A X-POPMail-Charset: English The Ramachandran plot shows the allowable values for the phi and psi angles at each alpha carbon in a protein chain. What puzzles me is that there are 3 distinct, unconnected areas on the plot, for right and left handed helices, and for beta sheets. All other regions are claimed to be sterically impossible. But this would imply that smooth variation of phi and psi during folding may be impossible, because the random coil values would all presumably be somewhere in the beta sheet region, but some residues would need to move to the right and left hand alpha helix regions, moving through disallowed "no man's land" values. Obviously there are assumptions built into this whole model which are invalid, but I'm not sure where the problem lies. Any suggestions, please! (The Ramachandran plot would make more sense if the allowed regions were merely preferred regions - energetically favorable.) Alan J. Robinson robin073@tc.umn.edu From owner-molec-model@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!feed1.news.luth.se!luth.se!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Jaap Heringa Newsgroups: bionet.molec-model Subject: PhD Studentship Available at NIMR, London Date: Wed, 14 Jan 1998 15:47:34 +0000 Organization: MRC Lines: 42 Message-ID: <34BCDE16.67F710B0@nimr.mrc.ac.uk> NNTP-Posting-Host: serine.nimr.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 6.2 IP22) A three-year Predoctoral MRC-funded Fellowship is available to UK-Citizens in the Division of Mathematical Biology, National Institute for Medical Research (NIMR), Mill Hill, London. Head of the Division is Dr Willie Taylor. The following is a short outline of the project: PROTEIN STRUCTURAL DOMAINS AND REPEATS; ANALYSIS AND PREDICTION FROM SEQUENCE INFORMATION ALONE The recognition of domains in protein structures is an important prerequisite for areas in protein science such as NMR-based structural elucidation and fold recognition. A number of empirical observations render domain prediction from only sequence information feasible, e.g., (i) domain interfaces show a.a. compositions intermediate to those of core and surface regions, (ii) domain linker regions display distinct compositions and (iii) domains in many proteins are (distant) repeats of a same basic sequence stretch. The project will embark on analysing existing databanks of protein domains and use the information to devise sequence profiles against which query sequences can be matched: A newly developed sensitive protein segment detection method SEGS by Willie Taylor will be of great use at this stage. Of help also will be the sensitive repeat detection method REPRO (see Heringa & Taylor, Curr. Opin. Struct. Biol. 7:416-421, 1997). All above information will be implemented in a computer method aimed at delineating domain boundaries in protein sequences. For more information, contact Dr Jaap Heringa Division of Mathematical Biology National Institute for Medical Research (NIMR) The Ridgeway, Mill Hill, London NW7 1AA, U.K. Tel.: +44 181 959 3666 ext. 2293 Fax : +44 181 913 8545 Email: jaap.heringa@nimr.mrc.ac.uk WWW : http://mathbio.nimr.mrc.ac.uk From owner-molec-model@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!not-for-mail From: Tom Chou Newsgroups: bionet.molec-model Subject: Pore-molecule binding constants? Date: Wed, 14 Jan 1998 11:53:41 +0000 Organization: DAMTP, University of Cambridge, UK. Lines: 29 Message-ID: <34BCA745.167E@damtp.cam.ac.uk> NNTP-Posting-Host: declaim.amtp.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V4.0 alpha) Dear molecular modelers: I am looking for some numbers. I would like to know what is the averaged energy (sum of interactions) of a single water molecule in bulk at STP relative to a typical, isolated water molecule inside a model (eg Gramicidin, etc) single-file, or nearly single-file pore. Ie, are pore interior attractive (energetically) to a water molecule relative to bulk (where H-bonding occurs?)? Are the energy differences large compared to kT? How about the same for a small ion such as Na+? Any specific example would be useful. Does anyone know of references? Cheers, Tom Chou DAMTP University of Cambridge Cambridge CB3 9EW ENGLAND From owner-molec-model@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!newsfeed.wli.net!feed.newsreader.com!portc03.blue.aol.com!newstf02.news.aol.com!newstf01.news.aol.com!audrey02.news.aol.com!not-for-mail From: squick2653@aol.com (SQuick2653) Newsgroups: bionet.molec-model Subject: J.D. Hanawalt Powder Diffraction Award Nominations Date: 15 Jan 1998 20:45:59 GMT Lines: 20 Message-ID: <19980115204500.PAA24619@ladder03.news.aol.com> NNTP-Posting-Host: ladder03.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com International Centre for Diffraction Data - www.icdd.com J.D. Hanawalt Powder Diffraction Award Nominations The International Centre for Diffraction Data is seeking nominees for the 1998 J.D. Hanawalt Powder Diffraction Award. The award is presented every three years for an important, recent contribution to the field of powder diffraction. The award consists of a citation and a cash gift of $1,000. The award recipient is expected to submit an abstract and present a paper on the work being recognized at an appropriate Powder Diffraction / Crystallographic Meeting. Recipient's travel expenses to the meeting will be provided. Work eligible for consideration must have been published after 1 January 1990. The selection committee welcomes suggestions, nominations, and documentation of accomplishments for possible recipients through 15 February 1998. Contact: Camden R. Hubbard - hubbardcr@ornl.gov Chairman Hanawalt Award Selection Committee c/o International Centre for Diffraction Data 12 Campus Boulevard Newtown Square, PA 19073-3273, U.S.A. From owner-molec-model@net.bio.net Thu Jan 15 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!usenet From: "David F. Green" Newsgroups: bionet.molec-model Subject: Re: Protein Folding Date: Thu, 15 Jan 1998 09:01:16 -0500 Organization: Massachusetts Institute of Technology Lines: 33 Message-ID: <34BE16AC.41C6@lms.mit.edu> References: <41125.robin073@tc.umn.edu> NNTP-Posting-Host: mycroft.lms.mit.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP22) Alan J. Robinson wrote: > suggestions, please! (The Ramachandran plot would make more sense if > the allowed regions were merely preferred regions - energetically > favorable.) > That's exactly what they are! You can think of a Ramachandran plot has being a slice through a 3-D plot - the "allowed" regions, being areas of low energy. The relative energies of various regions of the "disallowed" region differ between amino acids, with glycine generally having the lowest energy disallowed region. If you look at a Ramachandran plot showing the positions of amino acids in a real protein (e.g. Voet and Voet, "Biochemistry" 2nd ed. figure 7.8, Matthews and van Holde, "Biochemistry" 2nd ed. figure 6.10 ) you will see that in most proteins, there are amino acids with lie in "disallowed" regions of the Ramachandran plot. It's good that you posted this question - a lot of students have trouble understanding exactly what a Ramachandran plot means, and why some amino acids are allowed in the "disallowed" regions. You seem to have a good understanding of the concepts. Good luck in your studies! -- ************************************************ David F. Green Department of Chemistry Massachusetts Institute of Technology Cambridge, MA 02139 E-mail: dfgreen@lms.mit.edu Phone: (617) 228-6229 ************************************************ From owner-molec-model@net.bio.net Thu Jan 15 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!newsfeed.nacamar.de!newsfeed.eerie.fr!jussieu.fr!not-for-mail From: Pierre Tuffery Newsgroups: bionet.molec-model Subject: XmMol 3.1 release Date: Fri, 16 Jan 1998 10:13:55 +0000 Organization: INSERM U155, Centre de Bioinformatique, Universite Paris 7 Lines: 27 Message-ID: <34BF32E3.42B@urbb.jussieu.fr> NNTP-Posting-Host: jabiru.urbb.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; HP-UX B.10.20 9000/780) This is to announce the release of XmMol 3.1, a desktop tool for molecular visualization. The distribution is now made via the web instead of the ftp server: http://duc.urbb.jussieu.fr/XmMol.html =========================================================== What is new in XmMol 3.1 - Much enhanced interface with Raster3D and MolScript to reach a quick and simple preparation of cartoons including different representations. - The possibility to manage files including different molecular types (DNA, Proteins, ...). - The possibility to have different representation types at the same time for fragments of a same file (a consequence of the previous point). - Enhanced documentation (2 postscript manuals included). - New delegates but also deep modification of some commands that will need an adaptation of the delegates used with the previous versions. - Enhanced ablity for non PseudoColor displays. This was done, as for previous versions, with the aim to keep XmMol a desktop tool easy to use, that should allow 'ad lib' colouring, atom display and rendering selection. =========================================================== From owner-molec-model@net.bio.net Thu Jan 15 22:00:00 1998 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.molec-model Subject: Hydration Energy of Single Amino Acids Date: 16 Jan 1998 17:07:21 GMT Organization: Vollum Institute Lines: 12 Distribution: world Message-ID: <69o449$5sb$1@fremont.ohsu.edu> NNTP-Posting-Host: 137.53.99.48 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXDate: Fri, 16 Jan 1998 17:14:47 GMT Hi all, Can someone please give me a reference on the hydration energy of amino acids in solution, not incorporated into proteins? I have a paper by Beveridge and colleagues from several years ago, modelling the hydration of glycine zwitterion. However, I need to know what sorts of range exists and whether smaller amino acids are more or less hydrated than larger ones. Thanks, Matt Jones From owner-molec-model@net.bio.net Sun Jan 18 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!131.103.1.114!news1.chicago.iagnet.net!iagnet.net!mr.net!newshub.tc.umn.edu!newsstand.tc.umn.edu!usenet From: "Alan J. Robinson" Newsgroups: bionet.molec-model Subject: Re: Protein Folding Date: Mon, 19 Jan 98 13:35:56 CST Organization: University of Minnesota Lines: 22 Message-ID: <61238.robin073@tc.umn.edu> NNTP-Posting-Host: pub-20-b-152.dialup.umn.edu X-Minuet-Version: Minuet1.0_Beta_18A X-POPMail-Charset: English I would like to thank all those who replied to my post about the signficance of the Ramachandran plot and whether it is consistent with the folding process. I haven't had time to fully research this, but I'm now led to believe that Ramachandran's original figure was based on a simplified computer model of a polypeptide, with equal values for phi and for psi at each consecutive residue. This more or less corresponds to the interior of secondary structure in native folded proteins. Thus the Ramachandran plot is roughly what secondary structure is sterically possible in folded proteins, even before hydrogen bonding takes place. Real proteins are obviously more complex than this in several different ways, so that the values of phi and psi observed in practice don't always fall within the regions shown on the plot, and certainly don't constrain the folding process itself in any direct way (though obviosuly constrained by steric considerations too.) Alan J. Robinson robin073@tc.umn.edu From owner-molec-model@net.bio.net Mon Jan 19 22:00:00 1998 Path: biosci!GATE.SINICA.EDU.TW!ccchuang From: ccchuang@GATE.SINICA.EDU.TW (Chyh-chong Chuang) Newsgroups: bionet.molec-model Subject: grasp, how to? (1) Date: 19 Jan 1998 18:19:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Grasp experts: I am a new grasp user. I hope to produce two kinds of representation of my molecules in grasp. I had tried, but I still don't get the way. I have two different protein structures superimposed. (1) I built molecular surface and mapped potential to surface for each protein. I am plan to represent the surface of protein 1 in left, and surface of protein 2 in right. But I still don't try out to do so. Could Someone give me some hints to do so? (2) And I plan to label certain residues in the sueface, but I did not find way to do so. Is it possible in grasp? Thanks all for help! ccchuang ============================================ Chyh-Chong Chuang Institude of Biological Chemistry, Academia Sinica,Taipei, Taiwan -------------------------------------------- Phone: 886-2-7858981 ext 7091 Fax: 886-2-7883473 E-Mail: ccchuang@gate.sinica.edu.tw ============================================ From owner-molec-model@net.bio.net Mon Jan 19 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!ais.net!news-out.internetmci.com!newsfeed.internetmci.com!204.156.128.20!news1.best.com!noos.hooked.net!news.hooked.net!not-for-mail From: "genomik" Newsgroups: bionet.molec-model Subject: New Website for jobs in Molec-model, Genomics, BioInformatics Date: Tue, 20 Jan 1998 05:13:20 -0800 Organization: Hooked Online Services Lines: 5 Message-ID: <6a2809$ind$1@its.hooked.net> NNTP-Posting-Host: italy-55.ppp.hooked.net X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Nice Links too www.genomejobs.com Check it out From owner-molec-model@net.bio.net Thu Jan 22 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!hecate.umd.edu!not-for-mail From: Eugene Melamud Newsgroups: bionet.molec-model Subject: Re: grasp, how to? (1) Date: Fri, 23 Jan 1998 12:25:07 -0500 Organization: CARB Lines: 43 Message-ID: <34C8D273.446B@carb.nist.gov> References: NNTP-Posting-Host: chipotle.carb.nist.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) To: Chyh-chong Chuang Try : http://tincan.bioc.columbia.edu/Lab/grasp/grasp_contents.html#7.1 Chyh-chong Chuang wrote: > > Dear Grasp experts: > > I am a new grasp user. I hope to produce two kinds of > representation of my molecules in grasp. I had tried, but I still don't > get the way. > I have two different protein structures superimposed. > > (1) I built molecular surface and mapped potential to surface for each > protein. I am plan to represent the surface of protein 1 in left, and > surface of protein 2 in right. But I still don't try out to do so. Could > Someone give me some hints to do so? > (2) And I plan to label certain residues in the sueface, but I > did not find way to do so. Is it possible in grasp? > > Thanks all for help! > > ccchuang > > ============================================ > Chyh-Chong Chuang > Institude of Biological Chemistry, > Academia Sinica,Taipei, Taiwan > -------------------------------------------- > Phone: 886-2-7858981 ext 7091 > Fax: 886-2-7883473 > E-Mail: ccchuang@gate.sinica.edu.tw > ============================================ -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Eugene Melamud Email: melamud@carb.nist.gov Tel : 1-301-738-6240 _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-molec-model@net.bio.net Mon Jan 26 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molec-model Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 27 Jan 1998 02:00:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801271000.CAA14487@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! 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The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-molec-model@net.bio.net Tue Jan 27 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.molec-model Subject: Your Web Site Re-Launch Date: 28 Jan 1998 17:04:32 -0000 Lines: 83 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6anof0$5nn@mserv1.dl.ac.uk> Reply-To: launch@LAUNCHMASTER.COM Original-To: molmodel@dl.ac.uk To: molmodel@daresbury.ac.uk Need a re-launch? Launchmaster will re-launch your web site to 50 search engines and indexes for $95. Satisfaction guaranteed! Millions of people use search engines to find web sites every day. But if your site isn't listed, no one will find it. Launchmaster will re-launch your site by submitting it to the top 50 search engines for $95. Here's how to do it: 1. Complete the form below and return it to us. 2. 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(This information will be posted to the search engines/indexes): Contact name: Company Name: Address: City: State/Prov: Zip/Postal Code: Telephone: Fax: Email address: Contact e-mail address (in case we have questions about this order): URL: http:// Site Title: Description (250 characters): Key words (250 characters, in descending order of importance): If billing a different address, please complete the following: Addressee: Company Name: Address: City: State/Prov: Zip/Postal Code: Telephone: Fax: Email address: TERMS Terms are net 15 days from date of invoice. ______________________________________________________________________ Launchmaster, Inc. 12 Godfrey Place Wilton CT 06897 Phone: (203) 834-5823 Fax: (203) 834-1897 E-mail: launch@launchmaster.com From owner-molec-model@net.bio.net Wed Jan 28 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!worldnet.att.net!newsadm From: "Venkatesh Murthy" Newsgroups: bionet.molec-model Subject: Re: Protein Folding Date: Wed, 28 Jan 1998 19:23:42 -0500 Organization: AT&T WorldNet Services Lines: 34 Message-ID: <6aohtd$ov9@bgtnsc03.worldnet.att.net> References: <61238.robin073@tc.umn.edu> NNTP-Posting-Host: 12.68.114.85 X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Alan J. Robinson wrote in message <61238.robin073@tc.umn.edu>... >Real proteins are obviously more complex than this in several >different ways, so that the values of phi and psi observed in practice >don't always fall within the regions shown on the plot, and certainly >don't constrain the folding process itself in any direct way (though >obviosuly constrained by steric considerations too.) While Ramachandran outliers are observed in protein crystal structures, typically their numbers are smaller in higher resolution structures suggesting that, except in very rare cases, all amino acids must conform to the Ramachandran plot. This makes sense when you consider that the Ramachandran plot is primarily dependent (including favorable terms has very little effect overall) on the repulsive portion of the van der Waals potential. Two atoms simply cannot occupy the same space -- the electronic repulsions in dissallowed regions is much stronger than favorable forces at work in proteins. Simply put, except in exceptionally rare cases, Ramachandran outliers are more indicative of model errors than anything else. Also, Ramachandran did not use a computer model to generate the plot. The plot was calculated (and intuited) by hand. Finally, the plot is for a dipeptide, not a polypeptide. Venkatesh Murthy ------- MD/PhD Candidate Department of Biophysics & Biophysical Chemistry Johns Hopkins University School of Medicine From owner-molec-model@net.bio.net Sat Jan 31 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!209.150.160.22!newsfeed.wli.net!nntp.flash.net!news-feeder.onramp.net!news.onramp.net!not-for-mail From: "Cynthia S. 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