From chemistry-request@server.ccl.net Tue Mar 4 18:26:40 2003 Received: from students.iit.edu ([216.47.143.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h24NQeR15063 for ; Tue, 4 Mar 2003 18:26:40 -0500 Received: by students.iit.edu (5.1.053) id 3E6069070001E83B; Tue, 4 Mar 2003 17:19:18 -0600 Message-ID: <3E60690F000020AB@students.iit.edu> Date: Tue, 4 Mar 2003 17:19:18 -0600 In-Reply-To: <2283.128.32.27.14.1046803701.squirrel@nature.Berkeley.EDU> From: "Alfred Lee" Subject: RE: CCL:crystal modelling Reply-To: ayl@iit.edu To: "Dr. Mary V. O'Connor" , "computational chemistry" MIME-Version: 1.0 Importance: Normal Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h24NQgR15064 Mary: Two excellent books are: 1. Molecular Modeling Applications in Crystallization by Allan S. Myerson (ISBN: 0521552974) 2. Theoretical Aspects and Computer Modeling of the Molecular Solid State by Angelo Gavezzotti. (ISBN: 0471961876) Alfred -- Original Message -- > >Hello, CCLers: > > Does anyone have any specific book references that deal with >computational modelling of crystals and solids? The more detailed, >the better! > >Thanks, >Mary > >Mary V. O'Connor, Ph.D. >Rm. 235 Hilgard Hall >University of California >Berkeley, CA 94704 > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Mar 5 04:12:34 2003 Received: from dirf.bris.ac.uk ([137.222.10.72]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h259CXR26697 for ; Wed, 5 Mar 2003 04:12:33 -0500 Received: from sis.bris.ac.uk by dirf.bris.ac.uk with SMTP-PRIV with ESMTP; Wed, 5 Mar 2003 09:12:19 +0000 Received: from simpson (simpson.chm.bris.ac.uk [137.222.42.59]) by sis.bris.ac.uk (8.11.6/8.11.6) with SMTP id h259B7P17316 for ; Wed, 5 Mar 2003 09:11:07 GMT Message-ID: <000a01c2e2f8$75c33790$3b2ade89@chm.bris.ac.uk> From: Chris Arthur To: chemistry Subject: FLEXX and Autodock Validation Date: Wed, 5 Mar 2003 09:20:27 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C2E2F8.757FED00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C2E2F8.757FED00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Can anyone point me in the direction of any articles that discuss = validation studies of Flexx and/or autodock methodology? Thanks in advance Chris ------=_NextPart_000_0007_01C2E2F8.757FED00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Can anyone point me in the direction of = any=20 articles that discuss validation studies of Flexx and/or autodock=20 methodology?
 
Thanks in advance
Chris
------=_NextPart_000_0007_01C2E2F8.757FED00-- From chemistry-request@server.ccl.net Tue Mar 4 16:15:43 2003 Received: from mail.uvigo.es ([193.146.32.91]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h24LFhR05727 for ; Tue, 4 Mar 2003 16:15:43 -0500 Received: from mail.uvigo.es (localhost [127.0.0.1]) by mail.uvigo.es (8.12.8/8.12.1) with ESMTP id h24LFhEZ021707 for ; Tue, 4 Mar 2003 22:15:43 +0100 Received: from correo.uvigo.es (correo.uvigo.es [193.146.32.68]) by mail.uvigo.es (8.12.8/8.12.1) with ESMTP id h24LFd7E021702 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Tue, 4 Mar 2003 22:15:39 +0100 Received: from correo.uvigo.es (localhost [127.0.0.1]) by correo.uvigo.es (8.12.8/8.12.5) with ESMTP id h24LFcn0011109 for ; Tue, 4 Mar 2003 22:15:38 +0100 Received: from correo (correo [193.146.32.68]) by correo.uvigo.es (8.12.8/8.12.5) with ESMTP id h24LFYUf011100 for ; Tue, 4 Mar 2003 22:15:34 +0100 Date: Tue, 4 Mar 2003 22:15:34 +0100 (CET) From: "Silva Lopez; Carlos" X-X-Sender: To: Subject: NBO Analysis Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h24LFhR05728 Hello CCLers! I have done a NBO analysis of a transition structure were a sigma bond is being broken. The problem arises when check the orbital structure, there is still a pi bond where the sigma bond is already broken. Could it mean there is a certain aromaticity in that TS and pi electrons are still creating a "current" despite of the big bond distances. Is there any other point of view (with chemistry sense, not mathematical formulation of anything non graspable)? Thanks _-_-_-_-_-_-_-_-_-_-_-_- Carlos Silva López Dpto. Química Orgánica Universidade de Vigo Phone num: 0034 986812226 -_-_-_-_-_-_-_-_-_-_-_-_ From chemistry-request@server.ccl.net Wed Mar 5 07:18:41 2003 Received: from mail-a.bcc.ac.uk ([144.82.100.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h25CIfR20314 for ; Wed, 5 Mar 2003 07:18:41 -0500 Received: from pop-b.ucl.ac.uk by mail-a.bcc.ac.uk with SMTP (Mailer) with ESMTP; Wed, 5 Mar 2003 12:14:09 +0000 Received: from socrates-a.ucl.ac.uk (socrates-a.ucl.ac.uk [144.82.100.160]) by pop-b.ucl.ac.uk (8.11.6+Sun/8.9.3) with ESMTP id h25CE5q28155; Wed, 5 Mar 2003 12:14:05 GMT Date: Wed, 5 Mar 2003 12:14:05 +0000 (GMT) From: Graeme Day To: "Dr. Mary V. O'Connor" cc: computational chemistry Subject: Re: CCL:crystal modelling In-Reply-To: <2283.128.32.27.14.1046803701.squirrel@nature.Berkeley.EDU> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UCL-MailScanner: Found to be clean Dear Mary, For molecular crystals, three come to mind: A.I.Kitaigorodskii, Molecular Crystals and Molecules, Academic Press,1973 has some good chapters on modelling. A.J.Pertsin and A.I. Kitaigorodskii, The Atom-Atom Potential Method. Applications to Organic Molecular Solids, Springer-Verlag, 1987 more recently, there is A. Gavezzotti, Theoretical Aspects and Computer Modelling of the Molecular Solid State, John Wiley & Sons, 1997 Best wishes, Graeme --- Dr. Graeme M. Day Pfizer Institute for Pharmaceutical Materials Department of Chemistry University of Cambridge Lensfield Road, Cambridge, CB2 1EW gmd27@cam.ac.uk --- On Tue, 4 Mar 2003, Dr. Mary V. O'Connor wrote: > > Hello, CCLers: > > Does anyone have any specific book references that deal with > computational modelling of crystals and solids? The more detailed, > the better! > > Thanks, > Mary > > Mary V. O'Connor, Ph.D. > Rm. 235 Hilgard Hall > University of California > Berkeley, CA 94704 > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Mar 5 05:51:25 2003 Received: from evans.univer.kharkov.ua ([80.92.225.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h25ApKR13634 for ; Wed, 5 Mar 2003 05:51:20 -0500 Received: from spin.univer.kharkov.ua (spin.univer.kharkov.ua [192.168.213.252]) by evans.univer.kharkov.ua (8.12.6/8.12.5) with SMTP id h25ApHfS015547 for ; Wed, 5 Mar 2003 12:51:17 +0200 Received: by spin.univer.kharkov.ua with Microsoft Mail id <01C2E315.567E2080@spin.univer.kharkov.ua>; Wed, 5 Mar 2003 12:47:10 +0200 Message-ID: <01C2E315.567E2080@spin.univer.kharkov.ua> From: "sergey i. kotelevskii" To: "'CCL community'" Subject: FW: CCL:GAMESS error Date: Wed, 5 Mar 2003 12:47:08 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h25ApPR13640 ---------- From: sergey i. kotelevskii Sent: Wednesday, March 05, 2003 12:43 PM To: 'Gert von Helden' Subject: RE: CCL:GAMESS error ---------- From: Gert von Helden Sent: Wednesday, March 05, 2003 12:15 PM To: sergey i. kotelevskii Subject: Re: CCL:GAMESS error Dear Gert, Thank you very much. The molecular geometry was used as generated by another program. Indeed, I've got some progress due to cutting off extra digits. Curiously, I've thought of doing so this morning but... I was misleaded by the similar output from less symmetric structure like 1,2-oxazole. However, you are right: even in that case the symmetry group is Cs, not C1. To support the symmetry, all Z components should be discarded. Thank you once more. Sincerely, Serghey. Hi, Looking at the coordinates, they seem almost symmetric, however only almost. H 1.0 -2.04794 -0.83980 0.00039 H 1.0 2.04794 -0.83981 -0.00038 differ in y and z by 1e-5 A. Why don't you try with H 1.0 -2.04794 -0.83980 0.00039 H 1.0 2.04794 -0.83980 -0.00039 Otherwise, you have to look in the gamess manual how it wants the molecule to be oriented. Hope that helps, Gert -- ******************************************************* Dr. Gert von Helden FOM Institute for Plasmaphysics Rijnhuizen Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands http://www.rijnh.nl/ e-mail: gertvh@rijnh.nl phone: (+31) 30 6096999, fax: (+31) 30 6031204 From chemistry-request@server.ccl.net Mon Mar 3 21:26:29 2003 Date: Thu, 27 Feb 2003 17:35:04 -0800 From: Shi-Yi Liu Message-ID: <27022003173504-jkl-resent@janice.schrodinger.com> To: chemistry@ccl.net Subject: New release of Schrodinger software Schrodinger is pleased to announce a new release of its software products. The release, including FirstDiscovery 2.5, Jaguar 5.0, MacroModel 8.1, and Maestro 5.1, contains many new features and enhancements. In particular, Glide 2.5, the ligand-receptor docking module of FirstDiscovery, demonstrates significant improvement in library screening through the incorporation of new scoring functions and a new extra-precision mode. For more information about the new release, or to obtain an evaluation copy of the software, please visit www.schrodinger.com. From chemistry-request@server.ccl.net Wed Mar 5 11:19:27 2003 Received: from antivirus2.its.rochester.edu ([128.151.57.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h25GJRa07307 for ; Wed, 5 Mar 2003 11:19:27 -0500 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.12.8/8.12.4) with ESMTP id h25GJQDA015940 for ; Wed, 5 Mar 2003 11:19:27 -0500 (EST) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.12.8/8.12.4) with SMTP id h25GJQRs015935 for ; Wed, 5 Mar 2003 11:19:26 -0500 (EST) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.8/8.12.1) with ESMTP id h25GJPiZ020531 for ; Wed, 5 Mar 2003 11:19:25 -0500 (EST) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: Excited state MD simulation Date: Wed, 5 Mar 2003 11:17:02 -0500 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200303051117.02770.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h25GJRa07308 Dear All: Could anybody point me to some references about doing Excited state MD simulation? both the classical or QM methods are ok. wei zhuang From chemistry-request@server.ccl.net Wed Mar 5 12:59:58 2003 Received: from smtp.unc.edu ([152.2.1.242]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h25Hxva15671 for ; Wed, 5 Mar 2003 12:59:58 -0500 Received: from login0.isis.unc.edu (login0.isis.unc.edu [152.2.1.97]) by smtp.unc.edu (8.12.2/8.12.2) with ESMTP id h25HxK00029331 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 5 Mar 2003 12:59:20 -0500 (EST) Date: Wed, 5 Mar 2003 12:59:20 -0500 (EST) From: Iosif Vaisman X-X-Sender: ivaisman@login0.isis.unc.edu To: chemistry@ccl.net Subject: ACS Short Course in Computational Chemistry and Computer-Assisted Drug Design Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ACS Short Course Computational Chemistry and Computer-Assisted Drug Design: Practical Approaches 225th ACS National Meeting New Orleans, Ernest N. Morial Convention Center Friday-Saturday, March 21-22, 2003 This introductory level course is designed for organic chemists, pharmaceutical chemists, and biochemists who are interested in learning more about computational and combinatorial methods, or scientists who need to develop a working knowledge of the fundamentals and need to understand the concepts and terminology of this rapidly developing area. Program Overview of Computational Chemistry and Computer-Assisted Drug Design Molecular Mechanics: Background, Development, Concepts, Force Fields Conformational Searching Molecular Dynamics Simulations: Background, Development, Concepts, and Applications Protein Structure Prediction Overview of Quantum Chemistry Methods and Its Application to Drug Design DNA and Protein Sequence and Structure Analysis Drug Design Methods and Pharmacophore Design QSAR and Property Prediction Methods 3D Database and 3D Searching Examples of Pharmacophore Perception and 3D Searching Combinatorial Chemistry and Chemical Diversity Concepts Faculty Phillip Bowen (U of Georgia), Osman Guner (Accelrys Inc.), Robert Pearlman (UT-Austin), Alexander Tropsha (UNC), Iosif Vaisman (GMU). The course will be taught from 9:00 a.m. to 5:00 p.m. on both days. If you have questions about the course, contact Dr. Bowen at (706) 542-2054 or at bowen@ccmsd.chem.uga.edu Registration Web: https://center.acs.org/applications/scr/scregister.cfm Email: shortcourses@acs.org Phone: 800-227-5558, ext. 4508, or 202-872-4508. From chemistry-request@server.ccl.net Wed Mar 5 13:05:42 2003 Received: from aguila.dti.udec.cl ([152.74.16.63]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h25I5ga16087 for ; Wed, 5 Mar 2003 13:05:42 -0500 Received: (qmail 3729 invoked from network); 5 Mar 2003 18:05:41 -0000 Received: from andes.dpi.udec.cl (HELO udec.cl) ([127.0.0.1]) (envelope-sender ) by 0 (qmail-ldap-1.03) with SMTP for ; 5 Mar 2003 18:05:41 -0000 Message-ID: <3E663C76.3070509@udec.cl> Date: Wed, 05 Mar 2003 15:05:42 -0300 From: "Dr. Antonio Buljan" User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en,pdf MIME-Version: 1.0 To: Andrew Ryzhkov , chemistry@ccl.net Subject: Re: CCL:G98w in DOS References: <3E65066C.4020802@udec.cl> <19214134156.20030304163129@zephyr.meteo.mcgill.ca> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Andrew: Your suggestion works pretty good! Antonio Andrew Ryzhkov wrote: >Dear Dr. Antonio Buljan, > >DAB> Someone knows as can be runed gaussian98w >DAB> under the interface MS-DOS of a PC? >DAB> I tries the following alternative: >DAB> g98 < file.gjf > file.out >DAB> g98w < file.gjf > file.out >DAB> but no works >DAB> Some suggestions? > >Just try the following command >c:\g98\g98.exe file.gjf > >The output file will be "file.out" > >Note that this will work only under Windows, in DOS box, >not in native DOS. > > > > From chemistry-request@server.ccl.net Wed Mar 5 14:36:40 2003 Received: from mxout4.cac.washington.edu ([140.142.33.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h25Jada23265 for ; Wed, 5 Mar 2003 14:36:39 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.32.139]) by mxout4.cac.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h25JaQLv014277; Wed, 5 Mar 2003 11:36:26 -0800 Received: from DGVR6B21 ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with SMTP id h25JaQaK004785; Wed, 5 Mar 2003 11:36:26 -0800 Message-ID: <001201c2e34e$86008350$74805f80@DGVR6B21> From: "Carsten Detering" To: "Chris Arthur" , References: <000a01c2e2f8$75c33790$3b2ade89@chm.bris.ac.uk> Subject: Re: CCL:FLEXX and Autodock Validation Date: Wed, 5 Mar 2003 20:36:31 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01C2E356.E7BA3CF0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_000F_01C2E356.E7BA3CF0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Chris,=20 try these: Ha, S., Andreani, R., Robbins, A. and Muegge, I. J Comput Aided Mol Des = 14(5): 435-48.(2000).Evaluation of docking/scoring approaches: a = comparative study based on MMP3 inhibitors. Kramer, B., Rarey, M. and Lengauer, T. Proteins 37(2): = 228-41.(1999).Evaluation of the FLEXX incremental construction algorithm = for protein-ligand docking. Stahl, M. Persp. Drug Disc. Des. 20: 83-98.(2000).Modifications of the = scoring function in FlexX for virtual screening applications. Bissantz, C., Folkers, G. and Rognan, D. J. Med. Chem. 43: = 4759-4767.(2000).Protein-Based Virtual Screening of Chemical Databases. = 1. Evaluation of Different Docking/Scoring Combinations. Hope this helps, Carsten ------=_NextPart_000_000F_01C2E356.E7BA3CF0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Chris,
 
try these:
 

Ha, S., Andreani, R., Robbins, A. and Muegge, I. J Comput Aided = Mol=20 Des 14(5): 435-48.(2000).Evaluation of docking/scoring = approaches: a=20 comparative study based on MMP3 inhibitors.

Kramer, B., Rarey, M. and Lengauer, T. = Proteins=20 37(2): 228-41.(1999).Evaluation of the FLEXX incremental = construction=20 algorithm for protein-ligand docking.

Stahl, M. Persp. Drug Disc. Des. 20: = 83-98.(2000).Modifications=20 of the scoring function in FlexX for virtual screening = applications.

Bissantz, C., Folkers, G. and Rognan, D. J. Med. Chem. = 43:=20 4759-4767.(2000).Protein-Based Virtual Screening of Chemical Databases. = 1.=20 Evaluation of Different Docking/Scoring Combinations.

Hope this helps,

Carsten

 

------=_NextPart_000_000F_01C2E356.E7BA3CF0-- From chemistry-request@server.ccl.net Wed Mar 5 09:45:54 2003 Received: from igor.urz.unibas.ch ([131.152.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h25Ejqa32389 for ; Wed, 5 Mar 2003 09:45:54 -0500 Received: from unibas.ch ([131.152.94.93]) by igor.urz.unibas.ch (PMDF V6.1-1 #40761) with ESMTP id <0HBA00EM46CCEU@igor.urz.unibas.ch> for chemistry@ccl.net; Wed, 05 Mar 2003 15:45:48 +0100 (MET) Date: Wed, 05 Mar 2003 15:45:48 +0100 From: Michele Porro Subject: Scoring-Summary To: CCL Message-id: <278CD320-4F19-11D7-BFE2-000393913E54@unibas.ch> MIME-version: 1.0 (Apple Message framework v551) X-Mailer: Apple Mail (2.551) Content-type: multipart/alternative; boundary=Apple-Mail-3--151127998 X-Priority: 3 --Apple-Mail-3--151127998 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello everybody, first of all i would like to thank all of you, who=20 answer to my question. I really received a lot of contributions,=20 THANKS!! Best regards mike Here a list of the most cited papers on the argument "scoring" : B=F6hm, H.-J. (1994). "The development of a simple empirical scoring=20 function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure." J. Comp. Aid. Mol. Des. 8: 243-256. B=F6hm, H.-J. and M. Stahl (1999). "Rapid Empirical Scoring Functions in Virtual Screening Applications." Med. Chem. Res. 9(7/8): 445-462. Charifson, P. S., J. J. Corkery, et al. (1999). "Consensus Scoring: A=20 Method for Obtaining Improved Hit Rates from Docking Databases of=20 Three-Dimensional Structures into Proteins." J. Med. Chem. 42: 5100-5109. Eldridge, M. D., C. W. Murray, et al. (1997). "Empirical scoring=20 functions: I. The development of a fast empirical scoring funciton to estimate the binding affinity of ligands in receptor complexes." J. Comp. Aid. Mol.=20= Des. 11: 425-445. Gohlke, H., M. Hendlich, et al. (2000). "Knowledge-based Scoring=20 Function to Predict Protein-Ligand Interactions." J. Mol. Biol. 295: 337-356. Gohlke, H. and G. Klebe (2001). "Statistical potentials and scoring functions applied to protein-ligand binding." Curr. Opin. Struct. Biol.=20= 11: 231-235. Grzybowski, B. A., A. V. Ishchenko, et al. (2002). "=46rom = knowledge-based potentials to combinatorial lead design in silico." Acc Chem Res 35(5): 261-9. Muegge, I. and Y. C. Martin (1999). "A General and Fast Scoring=20 Funciton for Protein-Lignad Interactions: A Simplified Potential Approach." J. Med.=20= Chem. 42: 791-804. Muegge, I., Y. C. Martin, et al. (1999). "Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein." J Med Chem 42(14): 2498-503. Muegge, I. and M. Rarey (2001). Small Molecule Docking and Scoring.=20 Reviews in Computational Chemistry. K. B. Lipkowitz and D. B. Boyd. New York, Wiley-VCH. 17: 1-60. Tame, J. R. H. (1999). "Scoring functions: A view from the bench." J.=20 Com. Aid. Mol. Des. 13: 99-108. Oprea, T. I. and G. R. Marshall (1998). "Receptor-based Prediciton of=20 Binding Affinities." Persp. Drug Disc. Des. 9/10/11: 35-61. Halperin I, Ma B, Wolfson H and Nussinov R. "Principles of Docking: An=20= Overview of Search Algorithms and a Guide to Scoring Functions",=20 PROTEINS: Structure, Function, and Genetics, 2002; 47:409-443 Stahl, M.; Rarey, M. "Detailed Analysis of Scoring Functions for Virtual Screening" J. Med. Chem. 44(7) 2001 p1035 - 1042. Bissantz, C.; Folkers, G.; Rognan, D. "Protein-Based Virtual Screening=20= of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations." J. Med. Chem. 2000, 43, 4759 - 4767. "The Use of Scoring Functions in Drug Discovery Applications" Hans-Joachim Bohm and Martin Stahl Reviews in Computational Chemistry Vol 18, pp 41-87 Eds. Kenny B. Lipkowitz and Donald B. Boyd Wiley-VCH, 2002 Current Opinion in Structural Biology, Volume 11, Issue2, 1 April 2001,=20= pp. 231- 235. G. ... "Statistical potenetials and scoring functions=20 applied to protein-ligand binding." H Gohlke, G Klebe. Current Opinion in Chemical Biology, Volume5, issue4,1 august 2001, p.=20= 375 - 382. " High-throughput docking for lead generation" R Abagyan, M=20= Totrov. Il Farmaco, vol 57, issue3, March 2002, p. 243 - 251. "Identification=20 and mapping of small-molecule binding sites in proteins: computational=20= tools for structure-based drug design" C Sotriffer and G Klebe. H. Goelhke and G. Klebe (2002) Approaches to the description and=20 prediction of the binding affinity of small-molecule ligands to=20 macromolecular receptors, Angew.Chem.Int.Ed., 41, 2644-2676 Taylor, Jewsbury and Essex (2002) A review of protein-small molecule=20 docking methods, Journal of Computer-Aided Molecular Design, 16, 151-166 *************************************** Michele Porro Institute of Molecular Pharmacy Pharmacenter University of Basel Klingelbergstrasse 50 CH-4056 Basel Tel: +41 61 267 15 63 Fax: +41 61 267 15 52 e-mail: michele.porro@unibas.ch Web : www.pharma.unibas.ch **************************************** --Apple-Mail-3--151127998 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=ISO-8859-1 Hello everybody, first of all i would like to thank all of you, who answer to my question. I really received a lot of contributions, THANKS!! Best regards=20 mike Here a list of the most cited papers on the argument "scoring" : Times New RomanB=F6hm, H.-J. (1994). "The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure." J. Comp. Aid. Mol. Des. 8: 243-256. B=F6hm, H.-J. and M. Stahl (1999). "Rapid Empirical Scoring Functions in Virtual Screening Applications." Med. Chem. Res. 9(7/8): 445-462. Charifson, P. S., J. J. Corkery, et al. (1999). "Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins." J. Med. Chem. 42: 5100-5109. Eldridge, M. D., C. W. Murray, et al. (1997). "Empirical scoring functions: I. The development of a fast empirical scoring funciton to estimate the binding affinity of ligands in receptor complexes." J. Comp. Aid. Mol. Des. 11: 425-445. Gohlke, H., M. Hendlich, et al. (2000). "Knowledge-based Scoring Function to Predict Protein-Ligand Interactions." J. Mol. Biol. 295: 337-356. Gohlke, H. and G. Klebe (2001). "Statistical potentials and scoring functions applied to protein-ligand binding." Curr. Opin. Struct. Biol. 11: 231-235. Grzybowski, B. A., A. V. Ishchenko, et al. (2002). "From knowledge-based potentials to combinatorial lead design in silico." Acc Chem Res 35(5): 261-9. Muegge, I. and Y. C. Martin (1999). "A General and Fast Scoring Funciton for Protein-Lignad Interactions: A Simplified Potential Approach." J. Med. Chem. 42: 791-804. Muegge, I., Y. C. Martin, et al. (1999). "Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein." J Med Chem 42(14): 2498-503. Muegge, I. and M. Rarey (2001). Small Molecule Docking and Scoring. Reviews in Computational Chemistry. K. B. Lipkowitz and D. B. Boyd. New York, Wiley-VCH. 17: 1-60. Tame, J. R. H. (1999). "Scoring functions: A view from the bench." J. Com. Aid. Mol. Des. 13: 99-108. Oprea, T. I. and G. R. Marshall (1998). "Receptor-based Prediciton of Binding Affinities." Persp. Drug Disc. Des. 9/10/11: 35-61. Halperin I, Ma B, Wolfson H and Nussinov R. "Principles of Docking: An Overview of Search Algorithms and a Guide to Scoring Functions", PROTEINS: Structure, Function, and Genetics, 2002; 47:409-443 Stahl, M.; Rarey, M. "Detailed Analysis of Scoring Functions for Virtual Screening" J. Med. Chem. 44(7) 2001 p1035 - 1042. Bissantz, C.; Folkers, G.; Rognan, D. "Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations." J. Med. Chem. 2000, 43, 4759 - 4767. "The Use of Scoring Functions in Drug Discovery Applications" Hans-Joachim Bohm and Martin Stahl Reviews in Computational Chemistry Vol 18, pp 41-87 Eds. Kenny B. Lipkowitz and Donald B. Boyd Wiley-VCH, 2002 Current Opinion in Structural Biology, Volume 11, Issue2, 1 April 2001, pp. 231- 235. G. ... "Statistical potenetials and scoring functions applied to protein-ligand binding." H Gohlke, G Klebe. Current Opinion in Chemical Biology, Volume5, issue4,1 august 2001, p. 375 - 382. " High-throughput docking for lead generation" R Abagyan, M Totrov.=20 Il Farmaco, vol 57, issue3, March 2002, p. 243 - 251. "Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design" C Sotriffer and G Klebe. H. Goelhke and G. Klebe (2002) Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors, Angew.Chem.Int.Ed., 41, 2644-2676 Taylor, Jewsbury and Essex (2002) A review of protein-small molecule docking methods, Journal of Computer-Aided Molecular Design, 16, 151-166 *************************************** Michele Porro Institute of Molecular Pharmacy Pharmacenter University of Basel Klingelbergstrasse 50 CH-4056 Basel Tel: +41 61 267 15 63 Fax: +41 61 267 15 52 e-mail: michele.porro@unibas.ch Web : www.pharma.unibas.ch **************************************** --Apple-Mail-3--151127998-- From chemistry-request@server.ccl.net Wed Mar 5 12:13:35 2003 Received: from anor.ics.muni.cz ([147.251.4.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h25HDYa11974 for ; Wed, 5 Mar 2003 12:13:34 -0500 Received: from bilbo.chemi.muni.cz (bilbo.chemi.muni.cz [147.251.28.2]) by anor.ics.muni.cz (8.12.1/8.12.1) with ESMTP id h25HDXj1000377 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NO) for ; Wed, 5 Mar 2003 18:13:33 +0100 Received: from pegas (pegas.chemi.muni.cz [147.251.28.96]) by bilbo.chemi.muni.cz (8.11.6/8.8.5) with ESMTP id h25HDXc28060 for ; Wed, 5 Mar 2003 18:13:33 +0100 (MET) Message-ID: <00b601c2e33b$5a53c450$601cfb93@chemi.muni.cz> Reply-To: =?iso-8859-2?Q?Michal_Boh=E1=E8?= From: =?iso-8859-2?Q?Michal_Boh=E1=E8?= To: Subject: Delphi Calculation of interaction energies Date: Wed, 5 Mar 2003 18:19:17 +0100 Organization: NCBR MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00B3_01C2E343.BBFE3BB0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 X-Muni-Virus-Test: Clean This is a multi-part message in MIME format. ------=_NextPart_000_00B3_01C2E343.BBFE3BB0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable Hi everybody, Currently I'm solving the problem of calculation of the electrostatic=20 interaction energies between two distant charged residues in the = protein.=20 I had found the theoretical possibility of such calculation including = the=20 solvent effect using the PB equation in the Delphi package as is shown = in=20 the its examples of Subtilisin (example from version 3.0).=20 I have crucial question concerning this proposed methodology: =20 I would like to calculate the electrostatic interaction between all = charged=20 residues and halide ion, which is noncovalently bound in the active site = of the haloalkane dehalogenase protein. Halide is hetero-atom in this = case being an intermediate of the enzymatic reaction. I'm trying to find its stabilization by charged protein residues... Is it possible to perform such calculations with heteroatom using = current=20 Delphi 4.0 package? I would like to include into the active also two=20 experimentally known catalytic waters (essential for hydrolysis), = affecting=20 the electrostatics of the enzyme active site....is it possible to = include them too? Does anyone have any more experiences in calculation of such = electrostatic interactions using using Delphi? If anyone will be interested in this = general=20 question I can write him more details concerning this study.=20 Any comments and ideas or help will be greatly acknowledged ;-) Best regards, Michal =20 ************************************************************** Michal Boh=E1=E8, MSc. ************************************************************** student at National Centre for Biomolecular Research Faculty of Science, Masaryk University Kotl=E1=F8sk=E1 2, 611 37, Brno Czech Republic email: bogey@chemi.muni.cz URL: http://ncbr.chemi.muni.cz/~bogey phone: +420-541129377 fax: +420-541129506 cell: +420-604747103 ------=_NextPart_000_00B3_01C2E343.BBFE3BB0 Content-Type: text/html; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable
Hi everybody,
Currently I'm solving the = problem of=20 calculation of the electrostatic
interaction energies = between two distant charged residues in = the protein.=20
I had found the theoretical possibility of such = calculation=20 including the
solvent effect using the PB=20 equation in the Delphi = package as is shown in =
the its examples of=20 Subtilisin (example from=20 version 3.0).
 
I have crucial question = concerning=20 this proposed methodology:
 
I would like = to calculate the=20 electrostatic interaction between all charged
residues and halide ion, = which is=20 noncovalently bound in = the active=20 site
of the haloalkane = dehalogenase protein.=20 Halide is hetero-atom in this case
being an intermediate of the = enzymatic=20 reaction. I'm trying to find its
stabilization by charged = protein=20 residues...
Is it possible to perform = such=20 calculations with = heteroatom using=20 current
Delphi 4.0 package? I would = like to=20 include into the active also two
experimentally known = catalytic waters (essential for = hydrolysis),=20 affecting
the electrostatics = of the enzyme active site....is it = possible to=20 include them too?
 
Does anyone have any more = experiences in=20 calculation of such electrostatic
interactions using using = Delphi?  If anyone = will be=20 interested in this general
question I can write him more details concerning = this study.=20
Any comments and = ideas or help will=20 be greatly acknowledged=20 ;-)
 
Best regards,
Michal
 
**************************************************************  =20 Michal Boh=E1=E8,=20 MSc.
**************************************************************
   student = at
   National Centre = for=20 Biomolecular Research
   Faculty of Science, Masaryk=20 University
   Kotl=E1=F8sk=E1 2, 611 37, = Brno
   Czech=20 Republic
 
   email: bogey@chemi.muni.cz
 &nbs= p;=20 URL:   http://ncbr.chemi.muni.cz/~boge= y
  =20 phone: +420-541129377
   fax:  =20 +420-541129506
   cell: =20 +420-604747103
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