From owner-chemistry@ccl.net Tue May 27 03:09:01 2008 From: "Andreas Klamt klamt[a]cosmologic.de" To: CCL Subject: CCL: software for plotting hydrophobic interactions Message-Id: <-37040-080527030625-26618-2hQZ+RF71l3bthYGcDRFJA|*|server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 27 May 2008 09:06:11 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt^-^cosmologic.de] Dear Arthur, our COSMO-RS method clearly explains hydrophobicity as an effective entropic interaction, arising from the balance of polar, hydrogen-boding, and dispersive interactions in the solvent and between solvent and solute. Thus it identifies hydrophobic interactions by the polarization charge density sigma arising from DFT/COSMO calculations. These surface charge densities can be vividly visualized as VRMLs (see http://www.cosmologic.de/LifeScience/visualization_LS.html or see my book (Klamt, COSMO-RS: From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design, Elsevier 2005) The green areas are most hydrophobic. The hydrohobic range fades out into light blue and light yellow. This is a way to visualize hydrophobic regions on the most fundamental basis as possible. Regards Andreas Arthur computationalboy|*|gmail.com schrieb: > Dear all: > Can anyone recommend software for displaying hydrophobic interactions? > I know ligplot and ligandexplorer can do this. However, I need some > others. > Thanks in advance! > > -- > Arthur J. Wang > Shenyang Pharmaceutical University P.O. Box 40 > 103 Wenhua Road, Shenhe District > Shenyang,110016, P. R. China > Tel : +86 24 23986419 > Fax: +86 24 23995043 > E-Mail: wjmed(at)126.com ; > computationalboy(at)gmail.com -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt[]cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- Please note our COSMO-RS Symposium in 2009 (For details see: http://www.cosmologic.de/Symposium/symposium.html) From owner-chemistry@ccl.net Tue May 27 05:27:01 2008 From: "Dr. Sudhir A. Kulkarni sudhirk]=[vlifesciences.com" To: CCL Subject: CCL: Software for molecular databank creation Message-Id: <-37041-080527004817-12050-vTNadJya0LVsAKS95FiKMQ],[server.ccl.net> X-Original-From: "Dr. Sudhir A. Kulkarni" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 27 May 2008 09:30:45 +0530 MIME-Version: 1.0 Sent to CCL by: "Dr. Sudhir A. Kulkarni" [sudhirk..vlifesciences.com] Look at Chemxplor from MDS software that runs on windows system & creates databases from various file formats. http://www.vlifesciences.com/vlife_tech/chemxplor.htm Sudhir andras.borosy__givaudan.com wrote: > I do not suggest ISIS Base, because it is very expensive. > > Better choices: > > 1. MOE (it is the best, but it is more expensive, because it offers much > more then a db manager): http://www.chemcomp.com > 2. Chemaxon: http://www.chemaxon.com/ > 3. Chemfinder: http://chemfinder.cambridgesoft.com/ > > Regards, > > Dr. András Péter Borosy > Scientific Modelling Expert > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf - > Switzerland > T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com > > > > > "Arthur computationalboy===gmail.com" > Sent by: owner-chemistry_._ccl.net > 22.04.2008 11:25 > Please respond to > "CCL Subscribers" > > > To > "Borosy, Andras " > cc > > Subject > CCL: Software for molecular databank creation > > > > > > > I just recommend MDL ISIS/Base, though it's commericially available! > > > Arthur, computationalboy_._gmail.com > 2008-04-22 > ----- Receiving the following content ----- > >> From: Michael Shokhen shokhen/a\mail.biu.ac.il >> > Receiver: Wang,Jian > Time: 2008-05-26, 17:00:15 > Subject: CCL: Software for molecular databank creation > > Sent to CCL by: "Michael Shokhen" [shokhen#%#mail.biu.ac.il] > Dear Colleagues, > > I want to collect information (molecular structure, biding affinity)about > inhibitors from literature and molecular databanks. My purpose is to > organize the collected data as input files for the following molecular > modeling and drug design. In other words I am looking for MS Windows > platform software tool for creation of my own molecular databank that can > read/write SD,SDF, XLS files format and then represent these data as a > table in MS Excel manner, where every field including molecular structures > will be active for editing. > I would appreciate if somebody can recommend me a relevant software. > Please dont mention the Accelrys Accord for Excel ! > > Thank you, > Michaelhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt--=_alternative 00447B72C1257455_Content-Type: text/html; charset="ISO-8859-1" > Content-Transfer-Encoding: quoted-printable > > >
I do not suggest ISIS Base, because > it is very expensive. >
>
Better choices: >
>
1. MOE (it is the best, but it is more > expensive, because it offers  much more then a db manager): http://www.chemcomp.com >
2. Chemaxon: http://www.chemaxon.com/ >
3. Chemfinder: http://chemfinder.cambridgesoft.com/ >
>
Regards, >
>
Dr. András Péter Borosy
> Scientific Modelling Expert
> Fragrance Research
> Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600 >  -  Dübendorf  -  Switzerland
> T:+41-44-824 2164  -  F:+41-44-8242926    -  http://www.givaudan.com >
>
>
>
> > >
"Arthur computationalboy===gmail.com" > <owner-chemistry_._ccl.net> >
Sent by: owner-chemistry_._ccl.net >

22.04.2008 11:25 > > >
>
Please respond to
> "CCL Subscribers" <chemistry_._ccl.net>
>
>

> > > > >
>
To
> 		"Borosy, Andras " > <andras.borosy_._givaudan.com> >
>
cc
> 		>
>
Subject
> 		CCL: Software for molecular databank > creation
>
> > >
>
>
>
>
>
I just recommend MDL ISIS/Base, though > it's commericially available! >
  >
  >
Arthur, computationalboy_._gmail.com >
2008-04-22 >
----- Receiving the following content > ----- >
From: Michael > Shokhen shokhen/a\mail.biu.ac.il > >
Receiver: Wang,Jian > >
Time: 2008-05-26, 17:00:15 >
Subject: CCL: Software for molecular > databank creation >
>
Sent to CCL by: "Michael Shokhen" > [shokhen#%#mail.biu.ac.il]
> Dear Colleagues,
>
> I want to collect information (molecular structure, biding affinity)about > inhibitors from literature and molecular databanks. My purpose is to organize > the collected data as input files for the following molecular modeling > and drug design. In other words I am looking for MS Windows platform software > tool for creation of my own molecular databank that can read/write SD,SDF, > XLS files format and then represent these data as a table in MS Excel manner, > where every field including molecular structures will be active for editing.
> I would appreciate if somebody can recommend me a relevant software.
> Please dont mention the Accelrys Accord for Excel !
>
> Thank you,
> Michael
>
>
> >
> E-mail to subscribers: CHEMISTRY_._ccl.net > or use:
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> > ------------------------------------------------------------------------ > > No virus found in this incoming message. > Checked by AVG. > Version: 7.5.524 / Virus Database: 269.24.1/1466 - Release Date: 5/25/2008 6:49 PM > From owner-chemistry@ccl.net Tue May 27 10:33:01 2008 From: "Gijs Schaftenaar schaft-x-cmbi.ru.nl" To: CCL Subject: CCL: 2nd call "International Computational Drug Discovery 2008" course. Message-Id: <-37042-080527102731-8170-2q6OkDNDGgVgGsaitoS4gw%server.ccl.net> X-Original-From: "Gijs Schaftenaar" Date: Tue, 27 May 2008 10:27:28 -0400 Sent to CCL by: "Gijs Schaftenaar" [schaft:+:cmbi.ru.nl] 2nd call "International Computational Drug Discovery 2008" course. The International Computational Drug Discovery course will take place from June 23 - July 4 2008, at Nijmegen, The Netherlands. We still have room for ten more participants. The course was developed by Computational Drug Discovery Group of the Centre of Molecular and Biomolecular Informatics (CMBI) of the Radboud University of Nijmegen in the Netherlands in collaboration with the pharmaceutical company Organon / Shering Plough. The two-week course describes some of the recent advances in drug discovery informatics, with a focus on the application of e-science to real life problems. The course is targeted at MSc and PhD students, and postdocs, who are interested in the field of computational target and drug discovery. The fee for the course is 100 euro. The course is financially supported by the dutch funding agency NBIC. Tripos supports the course with educational licenses for their Sybyl software. For more information see the course website (http://www.cmbi.ru.nl/ICDD2008/) or the flyer (http://www.cmbi.ru.nl/edu/bioinf4/ICDD2008.pdf) Sincerely Yours, Dr. Gijs Schaftenaar Dr. Sander Nabuurs Prof. Jacob de Vlieg From owner-chemistry@ccl.net Tue May 27 11:16:01 2008 From: "Danni L Harris danni_._simbiosys.ca" To: CCL Subject: CCL: software for plotting hydrophobic interactions Message-Id: <-37043-080527100552-6843-MctfRSDE1MLE+QRot1W6wg:+:server.ccl.net> X-Original-From: "Danni L Harris" Date: Tue, 27 May 2008 10:05:48 -0400 Sent to CCL by: "Danni L Harris" [danni!^!simbiosys.ca] Arthur, CheVi is a visualization package enabling you to display complementary interactions between ligand and receptor/protein (including hydrophobic regions). SPROUT is a package will enable you to visualize hydrophobic/ hydrogen-bonding regions of the protein pocket and then dock and score complimentary fragments to each of those regions, prior to 'tethering' with linkage elements. An assembled ligand may then be optimized and re-scored as re: interaction with the protein pocket. > "Arthur computationalboy|*|gmail.com" wrote: > > Sent to CCL by: Arthur [computationalboy__gmail.com] > ------=_Part_8698_20844372.1211847700447 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > Dear all: > Can anyone recommend software for displaying hydrophobic interactions? > I know ligplot and ligandexplorer can do this. However, I need some others. > Thanks in advance! > > -- > Arthur J. Wang > Shenyang Pharmaceutical University P.O. Box 40 > 103 Wenhua Road, Shenhe District > Shenyang,110016, P. R. China > Tel : +86 24 23986419 > Fax: +86 24 23995043 > E-Mail: wjmed(at)126.com ; > computationalboy(at)gmail.com > > ------=_Part_8698_20844372.1211847700447 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > Dear all:
Can anyone recommend software for displaying hydrophobic interactions?
I know ligplot and ligandexplorer can do this. However, I need some others.
Thanks in advance!

--
Arthur J. Wang
> Shenyang Pharmaceutical University P.O. Box 40
103 Wenhua Road, Shenhe District
Shenyang,110016, P. R. China
Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail: wjmed(at)126.com ;
> computationalboy(at)gmail.com > > ------=_Part_8698_20844372.1211847700447-- > > From owner-chemistry@ccl.net Tue May 27 11:53:02 2008 From: "Aleksey Kuznetsov AlexKuznetsov2007- -yandex.ru" To: CCL Subject: CCL: Turbomole: constrained optimization stops at the 3rd step Message-Id: <-37044-080526233606-16177-A56iytuT9Uxzz2A9XmVkjA~~server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 27 May 2008 07:35:52 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007---yandex.ru] Dear All, I am looking for a transition state in the reaction between H2 molecule and a complex of N2 molecule coordinated to a 4-atom transition metal cluster supported at MgO(100) surface. I use the constrained optimization with 1 internal coordinate fixed (distance between the transition metal atom and hydrogen atom). However, for two different values of the fixed internal coordinate I got the same problem: optimization stopped at the 3rd step at the relax stage, producing the following end of a job.3 file: MODTRACE: no modules on stack GETOLD : gradient mismatch ! relax ended abnormally relax step ended abnormally next step = relax RELAX termination criterium:=0 Could anybody please advise me what the problem here could be? I use the Turbomole version 5.7.1. Thank you very much in advance! With best regards, Aleksey Kuznetsov. ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: akuznets,euch4e.chem.emory.edu ------------------------------------------- From owner-chemistry@ccl.net Tue May 27 12:25:00 2008 From: "Lothar Terfloth lothar.terfloth()mol-net.com" To: CCL Subject: CCL: Software for molecular databank creation Message-Id: <-37045-080527120647-32388-sfdnNtxHobyD4rTIjrVxvw*_*server.ccl.net> X-Original-From: Lothar Terfloth Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 27 May 2008 17:06:54 +0200 MIME-Version: 1.0 Sent to CCL by: Lothar Terfloth [lothar.terfloth(0)mol-net.com] Hi Michael, I would like to direct your attention to the following links: a) Creating a Web-based, Searchable Molecular Structure Database Using Free Software http://merian.pch.univie.ac.at/%7Enhaider/cheminf/moldb.html b) MolDB4 http://merian.pch.univie.ac.at/%7Enhaider/cheminf/moldb4.html c) SDF Toolkit http://cactus.nci.nih.gov/SDF_toolkit/ The SDF Toolkit is a very useful tool to join structural data (SDFiles) with properties from CSV files. d) MN.Merge and MN.Table (Molecular Networks GmbH) http://www.molecular-networks.com/software/split_join_merge/index.html http://www.molecular-networks.com/software/table/index.html e) C=-=ROL (Molecular Networks GmbH) http://www.molecular-networks.com/software/category/warehousing.html With kind regards, Lothar Michael Shokhen shokhen/amail.biu.ac.il wrote: > Sent to CCL by: "Michael Shokhen" [shokhen#%#mail.biu.ac.il] > Dear Colleagues, > > I want to collect information (molecular structure, biding affinity)about inhibitors from literature and molecular databanks. My purpose is to organize the collected data as input files for the following molecular modeling and drug design. In other words I am looking for MS Windows platform software tool for creation of my own molecular databank that can read/write SD,SDF, XLS files format and then represent these data as a table in MS Excel manner, where every field including molecular structures will be active for editing. > I would appreciate if somebody can recommend me a relevant software. > Please dont mention the Accelrys Accord for Excel ! > > Thank you, > Michael> -- -------------------------------------------------------- Dr. Lothar Terfloth Tel. +49-9131-9790623 Molecular Networks GmbH Fax: +49-9131-815 669 Henkestr. 91 D-91052 Erlangen Germany email: Lothar.Terfloth=-=mol-net.com www: http://www.mol-net.com -------------------------------------------------------- From owner-chemistry@ccl.net Tue May 27 14:34:01 2008 From: "Dr David N Haney haney::edusoft-lc.com" To: CCL Subject: CCL: software for plotting hydrophobic interactions Message-Id: <-37046-080527142216-4587-Rf1BBcLvjlqmuxdxLwEUyg##server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 27 May 2008 10:52:32 -0700 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney,+,edusoft-lc.com] Dear Arthur, It in unclear from your post exactly what type of hydrophobic "display" you are looking for. HINT is a program that calculates both hydrophilic and hydrophobic values for molecule-molecule interactions. These values can be printed into an atom-atom interaction file. The information can also be visualized on a molecular graphics screen as a "field" using contour display capabilities. The HINT constants have been coorelated with free energy of binding for both protein-protein interactions as well as small ligand-protein docking interations. You should have a look at: http://www.edusoft-lc.com/hint/ 1. PROTEINS: (2001) 42:355–377. "Computationally Accessible Method for Estimating Free Energy Changes Resulting fromSite-Specific Mutations of Biomolecules: Systematic Model Building and Structural/ Hydropathic Analysis of Deoxy and Oxy Hemoglobins" 2. Eur. J. Med. (2007) 42:921-933. "The consequences of scoring docked ligand conformations using free energy correlations" And other references. On Tue, May 27, 2008 at 08:21:40AM +0800, Arthur computationalboy|*|gmail.com wrote: > Dear all: > Can anyone recommend software for displaying hydrophobic interactions? > I know ligplot and ligandexplorer can do this. However, I need some others. > Thanks in advance! > > -- > Arthur J. Wang > Shenyang Pharmaceutical University P.O. Box 40 > 103 Wenhua Road, Shenhe District > Shenyang,110016, P. R. China > Tel : +86 24 23986419 > Fax: +86 24 23995043 > E-Mail: wjmed(at)126.com ; > computationalboy(at)gmail.com -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney .. edusoft-lc.com # ################# ##################### From owner-chemistry@ccl.net Tue May 27 17:47:00 2008 From: "Carlos F. Lagos carlos*o*cbuc.cl" To: CCL Subject: CCL: software for plotting hydrophobic interactions Message-Id: <-37047-080527161746-24617-66xJgG2CraHJ45FhYyoAqg_-_server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 27 May 2008 16:33:51 -0300 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos..cbuc.cl] Try LigandScout (www.inteligand.com), it render 2D plot similar to those of Ligplot. QF Carlos Lagos A. Centre for Bioinformatics CB, Faculty of Biological Sciences Medicinal Chemistry Laboratory, Faculty of Chemistry P. Universidad Catolica de Chile Portugal # 49 - ZIP 6513492 Santiago - Chile Phone: + 56 2 6862269; http://www.cbuc.cl -----Mensaje original----- De: owner-chemistry _ ccl.net [mailto:owner-chemistry _ ccl.net] Enviado el: martes, 27 de mayo de 2008 14:53 Para: Lagos, Carlos F Asunto: CCL: software for plotting hydrophobic interactions Sent to CCL by: Dr David N Haney [haney,+,edusoft-lc.com] Dear Arthur, It in unclear from your post exactly what type of hydrophobic "display" you are looking for. HINT is a program that calculates both hydrophilic and hydrophobic values for molecule-molecule interactions. These values can be printed into an atom-atom interaction file. The information can also be visualized on a molecular graphics screen as a "field" using contour display capabilities. The HINT constants have been coorelated with free energy of binding for both protein-protein interactions as well as small ligand-protein docking interations. You should have a look at: http://www.edusoft-lc.com/hint/ 1. PROTEINS: (2001) 42:355-377. "Computationally Accessible Method for Estimating Free Energy Changes Resulting fromSite-Specific Mutations of Biomolecules: Systematic Model Building and Structural/ Hydropathic Analysis of Deoxy and Oxy Hemoglobins" 2. Eur. J. Med. (2007) 42:921-933. "The consequences of scoring docked ligand conformations using free energy correlations" And other references. On Tue, May 27, 2008 at 08:21:40AM +0800, Arthur computationalboy|*|gmail.com wrote: > Dear all: > Can anyone recommend software for displaying hydrophobic interactions? > I know ligplot and ligandexplorer can do this. However, I need some others. > Thanks in advance! > > -- > Arthur J. Wang > Shenyang Pharmaceutical University P.O. Box 40 > 103 Wenhua Road, Shenhe District > Shenyang,110016, P. R. China > Tel : +86 24 23986419 > Fax: +86 24 23995043 > E-Mail: wjmed(at)126.com ; > computationalboy(at)gmail.com -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney%x%edusoft-lc.com # ################# #####################http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt__________ NOD32 3135 (20080527) Information __________ This message was checked by NOD32 antivirus system. http://www.eset.com From owner-chemistry@ccl.net Tue May 27 19:17:01 2008 From: "=?EUC-KR?B?sei8vMiv?= shkim{}bmdrc.org" To: CCL Subject: CCL: software for plotting hydrophobic interactions Message-Id: <-37048-080527065303-27853-NqlLObDbIs3EQwL/8R3y5Q+/-server.ccl.net> X-Original-From: "=?EUC-KR?B?sei8vMiv?=" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 27 May 2008 18:56:38 +0900 MIME-Version: 1.0 Sent to CCL by: "=?EUC-KR?B?sei8vMiv?=" [shkim=-=bmdrc.org] Hi~ CCLer Poseview, This is very useful software on web. http://poseview.zbh.uni-hamburg.de/~poseview/poseview.php 2008/5/27 Arthur computationalboy|*|gmail.com : > Dear all: > Can anyone recommend software for displaying hydrophobic interactions? > I know ligplot and ligandexplorer can do this. However, I need some others. > Thanks in advance! > > -- > Arthur J. Wang > Shenyang Pharmaceutical University P.O. Box 40 > 103 Wenhua Road, Shenhe District > Shenyang,110016, P. R. China > Tel : +86 24 23986419 > Fax: +86 24 23995043 > E-Mail: wjmed(at)126.com ; > computationalboy(at)gmail.com