From marvin@iris51.biosym.com Tue Sep 20 20:59:03 1994 Received: from bioc1.biosym.com for marvin@iris51.biosym.com by www.ccl.net (8.6.9/930601.1506) id UAA15117; Tue, 20 Sep 1994 20:51:09 -0400 Received: from iris51.biosym.com by bioc1.biosym.com (5.64/0.0) id AA05539; Tue, 20 Sep 94 17:50:30 -0700 Received: by iris51.biosym.com (931110.SGI/930416.SGI) for @bioc1.biosym.com:CHEMISTRY@ccl.net id AA19582; Tue, 20 Sep 94 17:50:45 -0700 Date: Tue, 20 Sep 94 17:50:45 -0700 From: marvin@biosym.com (Marvin Waldman) Message-Id: <9409210050.AA19582@iris51.biosym.com> To: CHEMISTRY@ccl.net Subject: RE: SEAL Chris Chen asks: > Do anyone know any recent papers about SEAL calculation? Try: "An Alternative Method for the Alignment of Molecular Structures: Maximizing Electrostatic and Steric Overlap", Simon K. Kearsley and Graham M. Smith, Tetrahedron Computer Methodology, Vol. 3, No. 6C, pp. 615-633 (1990). Marvin Waldman, Ph.D. Manager, Life Sciences Product Development Biosym Technologies, Inc. e-mail: marvin@biosym.com From dec@proteus.co.uk Wed Sep 21 04:59:07 1994 Received: from eros.britain.eu.net for dec@proteus.co.uk by www.ccl.net (8.6.9/930601.1506) id EAA19821; Wed, 21 Sep 1994 04:12:46 -0400 Message-Id: <199409210812.EAA19821@www.ccl.net> Received: from proteus.co.uk by eros.britain.eu.net with UUCP id ; Wed, 21 Sep 1994 09:09:22 +0100 From: David Clark Date: Wed, 21 Sep 94 08:26:00 -0100 To: chemistry@ccl.net Subject: Ligand design talk Dear All A while back, the talk below was advertised on the list: The Chicago Computational Chemistry Club Presents Peter J. Zielinski Illinois Institute of Technology A New Method for Designing Ligands Thursday, September 8, 7:30 p.m. Room No. 1358, Tech Building, Department of Physics, Northwestern University, 2145 Sheridan Road, Evanston IL 60208. Now that the meeting has taken place, does anyone have any more details about the content of the talk for those who couldn't be present? Any notes, comments or references would be of interest. Many thanks David E. Clark From heelisp@newi.ac.uk Wed Sep 21 08:59:11 1994 Received: from dylan.newi.ac.uk for heelisp@newi.ac.uk by www.ccl.net (8.6.9/930601.1506) id IAA21696; Wed, 21 Sep 1994 08:29:55 -0400 Received: by dylan.newi.ac.uk (5.57/25-eef) id AA03207; Wed, 21 Sep 94 13:30:45 GMT From: Paul F Heelis Message-Id: <9409211330.AA03207@dylan.newi.ac.uk> To: chemistry@ccl.net Subject: entropy and hydration in MOPAC Date: Wed, 21 Sep 94 13:30:31 GMT Dear Netters, a couple of weeks ago I posted 2 questions 1 how can I do entropy calcs and simulate hydration using MOPAC. Here are the replies I recieved, many thanks to all. Paul Heelis, North East Wales Institute, UK Heelisp@NEWI.AC.UK =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry, aholder@vax1.umkc.edu 1. You need to perform a frequency claculation (FORCE) while using the keyword THERMO. 2. I think that MOPAC has the COSMO package present for solvations. I should note that we market the AMPAC package that does all of the things that MOPAC does, plus a lot more. AMPAC also has the AMSOL solvation methods developed by Truhlar and Cramer. These methods are usually considered better than COSMO. Following is an input and output file for water with the proper AMPAC (and I think MOPAC) options set. ps. Please do note that you need to make sure the geometry is optimized before you do the force calculation. N.B FROM PAUL HEELIS, I HAVE PUT THE SAMPLE FILE AT THE END OF THIS POSTING. I'm not sure what brand of MOPAC is shipping with ChemX, but I'm rel- atively sure it is dated. The versions of these public domain programs shipped witn other packages are uncertain, as the company has no reason (or expertise) to maintain them in a high quality fashion. To blow my own horn a bit, this is why we have begun to market AMPAC. It is all we do and it is simply the best package out there of its kind. The entropy calculations carried forth into Gibbs free energies are pretty reliable for AM1 (which I would much recommend over PM3). You can look at Holder, A. J.; Healy, E. F. THEOCHEM 1993, 23, 141 for some tables. I should note that the great majority of the energy of gas phase systems is in the enthalpy. Only in odd circumstances will energy differences in delta G be substantially different than energy differences in delta H. ********************************************************************** From steve trohalaki, wright patterson air force base "trohals@Picard.ml.wpafb.af.mil" I have recently looked into simulating hydration with the COSMO (Conductor-like Screening Model), which is in Mopac93 but not in Mopac6 - i'm not sure about version 6.43. COSMO is not a reaction field model but a continuum approach. alternatively, amsol, which is based on an older version of ampac (mopac and ampac are quite similar) adds free energy of solvation terms to the fock operator to account for hydration but you need the AM1 gas-phase energy of formation to get the free energy of solvation. amsol is available from qcpe, but i don't think it runs on macs. i'd be interested to hear the responses you receive. steve trohalaki, wright patterson air force base ********************************************************************** FROM wolfgang sauer "sauer@organik.uni-erlangen.de" for the inclusion of solvent effects in semiemp. calculation, I would suggest you'd have a look at our program VAMP. Besides the 'normal' AM1, PM3, MNDO and MINDO3 calcs and a few other unique features, there is the possibility to perform SCRF ("self consistent reaction field") calculations. Together with the possibility to combine it with CI ("configuration interaction"), you can evaluate the effects of solvents on both ground and excited states. At present, the following solvents are covered: n-hexane n-hexadecane carbon tetrachloride CCl4 benzene diethyl ether chloroform CHCl3 methylene chloride CH2Cl2 acetone ethanol acetonitrile dimethyl sulfoxide DMSO WATER pyridine nitrobenzene. For further information on VAMP or any of our other products, please contact our UK headquarters at Oxford Molecular The Magdlen Centre Oxford Science Park Oxford OX 4 4 GA Tel 0865 784 600 Fax 0865 784 601 or myself, as I am currently involved in the development of the next version of VAMP. Wolfgang Sauer Oxford Molecular - CCC Naegelsbachstr. 25 D-91052 ERLANGEN, FRG Tel : +49 9131 8796 0 Fax : +49 9131 8796 11 ********************************************************************* THIS IS THE SAMPLE AM1 ENTROPY CALC USING AMPAC. I REPEATED IT USING AM1 WITHIN MOPAC AND OBTAINED THE SAME RESULT. NOTE FROM PAUL HEELIS DAT file: AM1 force thermo(298,298) rot=2 PRECISE GRAD BONDS T=3600 WATER FOR TESTING PURPOSES O 0.000000 0 0.000000 0 0.000000 0 0 0 0 H 0.961270 1 0.000000 0 0.000000 0 1 0 0 H 0.961270 1 103.531481 1 0.000000 0 1 2 0 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 ------------ OUT file: ******************************************************************************* AM1 CALCULATION RESULTS ******************************************************************************* * AMPAC Version 5.0 * Presented by: * * Semichem, Inc. * 7128 Summit * Shawnee, KS 66216 * (913) 268-3271 * (913) 268-3445 (fax) * * FORCE - FORCE CALCULATION SPECIFIED * THERMO - THERMODYNAMIC QUANTITIES TO BE CALCULATED * ROT - SYMMETRY NUMBER OF 2 SPECIFIED * PRECISE - OPTIMIZATION CRITERIA TO BE INCREASED BY 10 TIMES, * - S.C.F. CRITERIA BY 100 TIMES, * - AND USE ACCURATE FINITE DIFFERENCE FORMULA IN HESSIAN * BONDS - FINAL BOND-ORDER MATRIX TO BE PRINTED * GRADIENTS- ALL GRADIENTS TO BE PRINTED * T= - A TIME OF 3600.0 SECONDS REQUESTED * AM1 - THE AM1 HAMILTONIAN TO BE USED ******************************************************************************* AM1 FORCE THERMO(298,298) ROT=2 PRECISE GRAD BONDS T=3600 WATER FOR TESTING PURPOSES ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES) (I) NA:I NB:NA:I NC:NB:NA:I NA NB NC 1 O 2 H 0.96127 * 1 3 H 0.96127 * 103.53148 * 1 2 CARTESIAN COORDINATES NO. ATOM X Y Z 1 8 0.0000 0.0000 0.0000 2 1 0.9613 0.0000 0.0000 3 1 -0.2249 0.9346 0.0000 MOLECULAR POINT GROUP SYMMETRY CRITERIA C2V 0.10000000 RHF CALCULATION, No. OF DOUBLY OCCUPIED LEVELS = 4 ** REFERENCES TO PARAMETERS ** H (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) O (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985) INTERATOMIC DISTANCES O 1 H 2 H 3 ------------------------------------------ O 1 0.000000 H 2 0.961270 0.000000 H 3 0.961270 1.510130 0.000000 STANDARD DEVIATION ON ENERGY (KCAL) 0.00000014509 STANDARD DEVIATION ON GRADIENT (KCAL/A,RD,RD) 0.00000890 0.00000000 0.00000000 HEAT OF FORMATION= -59.240786 KCAL/MOLE ( 0.05 SECONDS) RMS GRADIENT NORM= 0.001512 KCAL/MOLE/A ( 0.03 SECONDS) ORIENTATION OF MOLECULE IN FORCE CALCULATION: NO. ATOM X Y Z NO. ATOM X Y Z 1 8 0.0000 -0.0666 0.0000 2 1 0.0000 0.5283 0.7551 3 1 0.0000 0.5283 -0.7551 VIBRATIONAL FREQUENCIES AND ERRORS (CM-1), REDUCED FORCE CONSTANTS (MILLIDYNE/ANGSTROMS). DIPOLE DERIVATIVES (DEBYE/ANGSTROMS) AND NORMAL MODES (CARTESIAN COORDINATES). FREQ : 0.0 0.0 0.0 0.0 0.0 0.0 1885.5 3505.5 ERROR : 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.1 F-CST : 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 1.04733 3.62012 DIP(X): 0.000 0.000 0.000 0.000 0.000 0.627 0.000 0.000 DIP(Y): 0.000 0.000 0.000 0.000 0.000 0.000 -0.743 0.000 DIP(Z): 0.000 0.000 0.000 0.000 0.000 0.119 0.000 0.070 DIP TOT 0.000 0.000 0.000 0.000 0.000 0.638 0.743 0.070 1 0.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 2 0.0621 0.0000 0.5363 0.0000 0.0000 0.0000 -0.0706 0.0000 3 -0.2026 0.1323 0.0755 0.0007 0.0000 -0.1621 0.0000 0.0698 4 -0.5225 0.4435 0.1946 -0.0030 0.0000 0.9676 0.0000 0.0000 5 0.4023 0.5499 0.4096 0.0009 0.0000 -0.1183 0.5601 -0.4365 6 -0.4706 -0.3009 0.1753 0.0000 0.0000 -0.0689 -0.4287 -0.5541 7 0.0000 -0.0011 0.0000 1.0000 0.0000 0.0048 0.0000 0.0000 8 -0.2780 -0.5499 0.6630 -0.0009 0.0000 0.1183 0.5601 0.4365 9 -0.4706 -0.3009 0.1753 0.0000 0.0000 -0.0689 0.4287 -0.5541 FREQ : 3584.5 ERROR : 0.0 F-CST : 3.78511 DIP(X): 0.000 DIP(Y): -0.388 DIP(Z): 0.000 DIP TOT 0.388 1 0.0000 2 -0.0500 3 0.0000 4 0.0000 5 0.3970 6 0.5840 7 0.0000 8 0.3970 9 -0.5840 DESCRIPTION OF NORMAL MODES IN TERM OF BONDED INTERATOMIC DISTANCES VIB. 7 ATOMS O 1 AND H 2 SHIFT 0.76 ANGSTROMS 7.0% RADIALLY FREQ. 1885.51 O 1 H 3 0.76 7.0% VIB. 8 ATOMS O 1 AND H 2 SHIFT 0.76 ANGSTROMS 99.8% RADIALLY FREQ. 3505.48 O 1 H 3 0.76 99.8% VIB. 9 ATOMS O 1 AND H 2 SHIFT 0.74 ANGSTROMS 100.0% RADIALLY FREQ. 3584.48 O 1 H 3 0.74 100.0% ZERO POINT ENERGY: 12.83 KCAL/MOLE, ERROR: 0.000 MOLECULAR WEIGHT: 18.015200 AMU MOMENTS OF INERTIA IN 10**(-40)GRAM-CM**2: 2.960478 1.908372 1.052107 MOMENTS OF INERTIA (CM-1): 9.455661 14.668674 26.606876 SYSTEM IS A STABLE SPECIES CALCULATED THERMODYNAMIC PROPERTIES ASSUMING NO INTERNAL ROTATIONS. THERE ARE 3 GENUINE VIBRATIONS IN THIS SYSTEM TEMP. (K) PARTITION FUNCTION ENTHALPY HEAT CAPACITY ENTROPY CAL/MOL CAL/K/MOL CAL/K/MOL 298 VIB. 0.1000D+01 0.60125 0.01839 0.00224 ROT. 0.4349D+02 888.30522 2.98089 10.47797 INT. 0.4350D+02 888.90647 2.99928 10.48021 TRA. 0.7393D+26 1480.50870 4.96815 34.59088 TOT. 2369.41517 7.96743 45.07109 FULL COMPUTATION TIME : 1.530 SECONDS From groot@organon.akzonobel.nl Wed Sep 21 05:59:11 1994 Received: from apou01.akzonobel.nl for groot@organon.akzonobel.nl by www.ccl.net (8.6.9/930601.1506) id FAA20124; Wed, 21 Sep 1994 05:24:47 -0400 Received: by apou01.akzonobel.nl (5.65/AKZO-WvdL/940819) id AA15867; Wed, 21 Sep 1994 11:25:05 +0100 Received: by poppy.oss.akzonobel.nl (931110.SGI/930416.SGI) for @apou01.akzonobel.nl:chemistry@oscsunb.ccl.net id AA19096; Wed, 21 Sep 94 11:26:08 +0100 Date: Wed, 21 Sep 94 11:26:08 +0100 From: p.grootenhuis@organon.akzonobel.nl (Peter Grootenhuis) Message-Id: <9409211026.AA19096@poppy.oss.akzonobel.nl> To: chemistry@oscsunb.ccl.net Subject: CCL:Rotation Barriers in Alcohols Cc: groot@poppy.oss.akzonobel.nl Reply-To: p.grootenhuis@organon.akzonobel.nl "A friend of mine" is looking for conformations and intramolecular rotational barriers of alcohols, experimentally determined in aqueous solution. Of particular interest are ethanol, propanol, butanol, and glycol. Can anybody direct me to (un)published work in this area ? Thanks very much. -------------------------------------------------------------------------------- Dr. Peter D.J. Grootenhuis --- CMC dept. RK2330 --- N.V. Organon P.O. Box 20 --- 5340 BH Oss --- The Netherlands Phone: 31-4120-61920 --- Fax: 31-4120-62539 E-mail: p.grootenhuis@organon.akzonobel.nl -------------------------------------------------------------------------------- From C1790@SLVAXA.UMSL.EDU Wed Sep 21 11:59:16 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.9/930601.1506) id LAA26081; Wed, 21 Sep 1994 11:06:44 -0400 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.3-7 #2503) id <01HHDCC9063Q9YCGX4@SLVAXA.UMSL.EDU>; Wed, 21 Sep 1994 10:09:50 CDT Date: Wed, 21 Sep 1994 10:09:50 -0500 (CDT) From: BILL WELSH Subject: Structure of Taxol and Tamoxifen To: chemistry@ccl.net Message-id: <01HHDCC90FQW9YCGX4@SLVAXA.UMSL.EDU> X-VMS-To: in%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, Can someone point me to any articles which show the molecular structure of taxol and tamoxifen. Thanks. Bill Welsh Chemistry Dept. Univ. of Missouri-St. Louis From C1790@SLVAXA.UMSL.EDU Wed Sep 21 12:12:08 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.9/930601.1506) id LAA26025; Wed, 21 Sep 1994 11:04:40 -0400 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.3-7 #2503) id <01HHDC9IJ2N49YCGX4@SLVAXA.UMSL.EDU>; Wed, 21 Sep 1994 10:07:38 CDT Date: Wed, 21 Sep 1994 10:07:38 -0500 (CDT) From: BILL WELSH Subject: From Bill Welsh To: chemistry@ccl.net Message-id: <01HHDC9IKEV69YCGX4@SLVAXA.UMSL.EDU> X-VMS-To: in%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, Can someone give me the email address for contacting Clark Still (Columbia) if I have an inquiry regarding Macromodel? Thank you. Bill Welsh Dept. of Chemistry Univ. of Missouri-St. Louis From makula@bisance.citi2.fr Wed Sep 21 12:20:06 1994 Received: from FRMOP11.CNUSC.FR for makula@bisance.citi2.fr by www.ccl.net (8.6.9/930601.1506) id LAA26052; Wed, 21 Sep 1994 11:05:31 -0400 Received: from galaad.citi2.fr by FRMOP11.CNUSC.FR (IBM VM SMTP V2R2) with TCP; Wed, 21 Sep 94 17:03:41 EST Received: from bisance.citi2.fr by galaad.citi2.fr; (5.65/1.1.8.2/20Jun94-0455PM) id AA06317; Wed, 21 Sep 1994 16:55:57 +0200 Received: by bisance.citi2.fr (5.0/SMI-SVR4) id AA04504; Wed, 21 Sep 1994 17:04:39 --100 From: makula@bisance.citi2.fr (makula-bisance) Message-Id: <9409211504.AA04504@bisance.citi2.fr> Subject: "sparkles" in MOPAC To: chemistry@ccl.net Date: Wed, 21 Sep 1994 17:04:39 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1116 Dear Netters, I would like to calculate with MOPAC the geometry of an organic anion. I am not sure that the calculation of an ion alone in the gas-phase would be very realistic (mainly because of intramolecular electrostatic repulsion), so I tried to use the so-called "sparkles" which are defined in the MOPAC manual as "pure ionic charges" or more precisely as an "integer charge at the center of a repulsion sphere of form exp(-alpha*r)". The manual explains further that the sparkles can be used as counterions. Unfortunately, my MOPAC calculation with a positive sparkle "+" ended up with the positive charge almost superimposed on the atom of my anion bearing most of the negative charge. Have I missed something in the keyword specification ? does anybody have experienced this MOPAC feature with some success ? (some refs would be welcome ). I will summarize the answers for the net. Please use the following e-mail address (not the one in the From: line) if you want to answer directly to me: remi.le-goas@rp.fr Dr Remi Le Goas Computer Aided Molecular Design Rhone-Poulenc Agrochimie Lyon - FRANCE From rickl@iris118.biosym.com Wed Sep 21 12:59:23 1994 Received: from bioc1.biosym.com for rickl@iris118.biosym.com by www.ccl.net (8.6.9/930601.1506) id MAA27989; Wed, 21 Sep 1994 12:57:46 -0400 Received: from iris118.biosym.com by bioc1.biosym.com (5.64/0.0) id AA12488; Wed, 21 Sep 94 09:57:08 -0700 Received: by iris118.biosym.com (931110.SGI/930416.SGI) for @bioc1.biosym.com:chemistry@ccl.net id AA17892; Wed, 21 Sep 94 09:59:31 -0700 Date: Wed, 21 Sep 94 09:59:31 -0700 From: rickl@biosym.com (Rick Lee ) Message-Id: <9409211659.AA17892@iris118.biosym.com> To: dec@proteus.co.uk, chemistry@ccl.net Subject: Re: Inverse folding... >From: David Clark >Date: Tue, 13 Sep 94 14:16:44 -0100 >To: CHEMISTRY@ccl.net >Subject: CCL:Inverse folding/sequence threading/de novo folding software >Sender: chemistry-request@ccl.net >Errors-To: ccl@ccl.net >Precedence: bulk > > >Dear All > >Is anyone aware of any available software (commercial or otherwise) >for inverse protein folding/sequence threading or de novo folding? >I'm aware of TRIPOS' Matchmaker program but would be interested to >know of any others. > >Many thanks > >David E. Clark Biosym offers Profiles-3D, a program to assess the compatibility between amino acid sequences and three-dimensional structures. The program employs the method of David Eisenberg of UCLA, which analyzes structures in terms of the residues' local environments. Environments are classified in terms of secondary structure, solvent accessibility, and polar/apolar neighbors. Thus any 3D structure can be reduced to a 1D string of environment classes. After examining a set of well characterized globular proteins, a table of propensities for each of the 20 amino acids to be in each of the environment classes was developed. This 3D-1D scoring table can be used to measure a compatibility score and perform an alignment between a given sequence and structure. The scoring method can be used in 3 ways: 1) A single amino acid sequence can be compared to a database of pre-calculated 3D profiles (the environments for the structures combined with the scoring table). The database is comprised of all known structures from the Brookhaven PDB. This techniques is valuable for finding reference (template) structures from which to build homology models. 2) A given structure can be compared to a sequence database to study evolutionary relationships. 3) A built structure can be compared with its own sequence to assess the quality of the model. Since there are no insertions or deletions, the score needs no normalizing, and so it can be calculated on a residue by residue basis. Thus local areas of misfolding, or hotspots, can be identified. ================================================================ Richard H. Lee, Ph.D. (e-mail: rickl@biosym.com) Lead Scientist, Protein Modeling Biosym Technologies, Inc. Phone: (619) 546-5536 9685 Scranton Road Fax: (619) 458-0136 San Diego, CA 92121-2777 USA ================================================================ From emori@california.sandia.gov Wed Sep 21 14:01:46 1994 Received: from california.sandia.gov for emori@california.sandia.gov by www.ccl.net (8.6.9/930601.1506) id NAA28626; Wed, 21 Sep 1994 13:35:37 -0400 Received: by california.sandia.gov (8.6.9/1.15) id KAA18036; Wed, 21 Sep 1994 10:35:02 -0700 Date: Wed, 21 Sep 1994 10:35:02 -0700 From: emori@california.sandia.gov (mori eugenia) Message-Id: <199409211735.KAA18036@california.sandia.gov> To: C1790@SLVAXA.UMSL.EDU, chemistry@ccl.net Subject: Re: CCL:From Bill Welsh An e-mail address I have listed from July 1993 for Clark Still regarding Macromodel is mmod@cuchmc.chem.columbia.edu I must say that the one time I sent something there, I didn't get a reply, but I don't know if that was due to the address or not - Eugenia Mori Sandia National Labs / Livermore CA From noy@tci002.uibk.ac.at Wed Sep 21 14:04:51 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.9/930601.1506) id NAA28931; Wed, 21 Sep 1994 13:51:57 -0400 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA13752 (5.65c/IDA-1.4.4 for ); Wed, 21 Sep 1994 19:51:55 +0200 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA27576; Wed, 21 Sep 1994 19:51:53 +0200 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9409211751.AA27576@tci002.uibk.ac.at> Subject: dipeptides' coordinates To: chemistry@ccl.net Date: Wed, 21 Sep 1994 19:51:53 +0200 (DFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1096 Dear netters, One of my colleagues needs some dipeptides' coordinates for her works ( she is modelling interactions between dipeptides ). I have searched through the WEB space without success. It appears to me that most database on the internet maintain only proteins and big biomolecules. Does anybody know where I could get the coordinates for dipeptide somewhere ? Is there any database for them ? Any Ideas and suggestions are greatly appreciated. Thanks a lot in advance. best wishes, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci2.uibk.ac.at, noy@tci.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs ----------------------------------------------------------------------------- *** I have no past and no future. I just have today. From mwd@alamos.cray.com Wed Sep 21 14:05:44 1994 Received: from timbuk.cray.com for mwd@alamos.cray.com by www.ccl.net (8.6.9/930601.1506) id NAA28989; Wed, 21 Sep 1994 13:59:10 -0400 Received: from pajarito.cray.com (mwd@pajarito.cray.com [128.162.56.9]) by timbuk.cray.com (8.6.9/8.6.9L) with SMTP id MAA02910 for ; Wed, 21 Sep 1994 12:59:08 -0500 Received: by pajarito.cray.com (5.0/CRI-5.13) id AA07190; Wed, 21 Sep 1994 11:59:01 +0700 From: mwd@alamos.cray.com (Mark Dalton) Message-Id: <9409211759.AA07190@pajarito.cray.com> Subject: Re: Protein folding,structure prediction To: chemistry@ccl.net Date: Wed, 21 Sep 1994 11:58:59 -0700 (MDT) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 3103 For predicting 3D Structure of proteins from a primary sequence. (I still have a list of places to get 3D searching, i.e. comparison of 3D structures, if anyone needs the list). Thanks! Mark Here is the information I have: Steven Brenner - Has given a couple of presentations at various confernences on a package he has been working on. Steven is from Cambridge Univ. For predicting 3D structures from primary sequences. SeqSee - Science( 258:p1369) or ftp canopus.biochem.ualberta.ca A suite of programs for protein sequence analysis ProfileScan- forming a profile for given aligned sequences. by Michael Gribskov gribskov@sdsc.edu (formerly of one of the National Labs in the US). Scrutineer - a protein sequence motif analysis program You also may want to look into Scrutineer you can get it at: netserv@embl.bitnet Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. PNAS USA 84, 4355-4358. Gribskov, M., Methods in Enzymology (1990) 183, PP 146-159 URL = http://pscinfo.psc.edu/general/software/cray/c90/profiless/profiless.html PROFILE-SS is a program that combines the optimal local sequence alignment algorithm developed by Michael Watterman and Mark Eggert and the Profile analysis methods of Gribskov into one program that finds the N-best alignments between a database sequence and a profile. Bohr, H. and Bohr, J. and Brunak, S. and Cotterill, R. M. J. and Fredhom, H. and Lautrup, B. and Petersen, S. B. "A Novel Approach to Prediction of the 3-Dimensional Structures of Protein Backbones by Neural Networks", FEBS Letters. Vol. 261, 1990, pages 43-46 Fetrow, J. S.; Bryant, S. H. New programs for protein tertiary structure prediction. Bio/Technology 1993, 11, 479-484. Greller, L. D. and Steeg, E. W. and Salemme, F. R., "Neural Networks for the Detection and Prediction of 3D Structural Do mains in Proteins", Proceeedings Eighth International Conference on Mathematical and Computer Modelling. April, 1991. (A new version was submitted to Science). Goel, N., Rouyanian, B. and Sanati, M. 1982. On the computation of the tertiary structure of globular proteins. III. Interresidue distances andS computed structures. J. Theor. Biol. 99:705-757. Jameson, B.A. and Wolf, H. 1988. The antigenic index: a novel algorithm for predicting antigenic determinants. CABIOS 4:181-186. Janin, J. 1979. Surface and inside volumes in globular proteins. Nature 277:491-492. Wodak, S. J.; Rooman, M. J. Generation and testing protein folds. Curr. Opinion Struct. Biol. 1993, 3, 247-259. - Mark Dalton CH3-S-CH2 H H O H Cray Research,Inc. | | | \ | Los Alamos,NM 87544 CH2-C-COOH //\ ---C--CH2-C-COO C-CH2-C-COO mwd@cray.com | | || || | // | NH2 \\/ \ / CH NH3 O NH3 NH URL = http://lenti.med.umn.edu/~mwd/mwd.html From theochem@ctc.com Wed Sep 21 15:59:15 1994 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.9/930601.1506) id PAA01901; Wed, 21 Sep 1994 15:57:09 -0400 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA05489; Wed, 21 Sep 1994 15:59:28 -0400 Received: by eed02.ctc.com (920330.SGI/921111.SGI.AUTO) for @server1.ctc.com:mmodinfo@uoft02.utoledo.edu id AA18055; Wed, 21 Sep 94 15:56:49 -0400 From: theochem@ctc.com (Douglas Smith) Message-Id: <9409211956.AA18055@eed02.ctc.com> Subject: Call for Papers To: chemistry@ccl.net (Computational Chemistry List), mmodinfo@uoft02.utoledo.edu (MacroModel Mailing List) Date: Wed, 21 Sep 1994 15:56:48 -0500 (EDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2350 SYMPOSIUM ANNOUNCEMENT and Call for Papers Data Flow Programming and Visualization in Chemistry American Chemical Society Meeting Anaheim, CA April 2 - 7, 1995 Purpose: This symposium will focus on the use of data flow programming paradigms such as, but not limited to, AVS, Explorer, and Data Explorer for the rapid prototyping, development, and coding of tools used in computational chemistry, particularly for visualization. Presentations will include software development as well as applications. Sponsors: This symposium is jointly sponsored by the Computers in Chemistry Division of hte American Chemical Society and by the Molecular Graphics Society. The symposium will be part of the COMP division program at the Spring (April 2 - 7) 1995 meeting of the American Chemical Society in Anaheim, CA. Organizers: This symposium is organized by Dr. Douglas A. Smith of Concurrent Technologies Corporation, Dr. George Famini of ERDEC, U.S. Army, and Dr. Arthur Olson of the Scripps Institute. Publication of Proceedings: The sponsors have arranged to have papers based on the presentations published in a special issue of the Journal of Molecular Graphics. Interested parties should contact Dr. Smith using the information below as soon as possible. Abstracts of no more than 150 words should be supplied no later than October 20, 1994 on ACS abstract forms. You can obtain these forms by calling the ACS at 202-872-4396. -- Douglas A. Smith Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. +---------------------------------+---------------------------------+ | "The juvenile sea squirt wanders through the sea searching for | | a suitable rock or hunk of coral to cling to and make its home | | for life. For this task it has a rudimentary nervous system. | | When it finds its spot and takes root, it doesn't need its | | brain any more so it eats it. It's rather like getting tenure." | | --source unknown | +-------------------------------------------------------------------+ From stoutepf@chemsci1.es.dupont.com Wed Sep 21 18:59:23 1994 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.es.dupont.com by www.ccl.net (8.6.9/930601.1506) id SAA04326; Wed, 21 Sep 1994 18:02:13 -0400 Received: by gatekeeper.es.dupont.com; id AA01797; Wed, 21 Sep 94 18:02:07 -0400 Received: from [138.196.64.95] (chem95.es.dupont.com) by chemsci1.es.dupont.com (4.1/SMI-4.1) id AA00566; Wed, 21 Sep 94 17:59:21 EDT Message-Id: <9409212159.AA00566@chemsci1.es.dupont.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Reply-To: stoutepf@chemsci1.es.dupont.com X-Organization: The Du Pont Merck Pharmaceutical Company X-Mailer: Eudora 1.4 Date: Wed, 21 Sep 1994 18:01:52 -0500 To: chemistry@ccl.net, mwd@alamos.cray.com (Mark Dalton) From: stoutepf@chemsci1.es.dupont.com (Pieter Stouten) Subject: Re: CCL:Protein folding,structure prediction Mark Dalton wrote: >Scrutineer - a protein sequence motif analysis program >You also may want to look into Scrutineer you can get it at: > netserv@embl.bitnet > I am not sure anyone is still on bitnet :-). Just send mail to netserv@embl-heidelberg.de with the command "help" and you'll find out what they have to offer. Cheers, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Poul Anderson E-mail: stoutepf@chemsci1.es.dupont.com || Internet Shogi Server: kzinti ||