From chemistry-request@server.ccl.net Wed Sep 25 01:03:05 2002 Received: from kdmail2.netcologne.de ([194.8.194.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8P534721804 for ; Wed, 25 Sep 2002 01:03:04 -0400 Received: from cosmologic.de (xdsl-213-168-109-248.netcologne.de [213.168.109.248]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id BNP89195; Wed, 25 Sep 2002 07:02:13 +0200 (CEST) Message-ID: <3D91434F.6F29D49B@cosmologic.de> Date: Wed, 25 Sep 2002 07:02:07 +0200 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Richard Gillilan CC: Atte =?iso-8859-1?Q?Sillanp=E4=E4?= , chemistry@ccl.net Subject: Re: CCL:visualization of charges on surface References: <3D9085DD.6530B3CD@cornell.edu> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Just a short note: There is a very good visualization for COSMO screening charge densities "sigma" on COSMO surfaces available within our COSMOtherm software. For a lot of examples see http://www.cosmologic.de/visualization.html Sigma is the much more local and better measure of molecular surface polarity than ESP. Regards Andreas Klamt (Author of COSMO) Richard Gillilan schrieb: > > Atte Sillanpää wrote: > > > > Hello all, > > > > I'd like to plot the electrostatic potential on a cosmo cavity > > surface. I have performed the calculations using Turbomole, which has > > the GRID option to plot properties on 3D grids. This is where I get my > > potential. However, the surface, which in this case is the > > cosmo-cavity, on which I'd like to map the electrostatic potential, is > > defined by points in space, that is, their xyz-coordinates. Does > > anyone know of a program that is able to read these points and create > > the surface from it? > > You can use simple trilinear interpolation to map the potential values > > from the grid to the points (www.opendx.org can do this), but I assume the > real problem you have is that the points do not have a connection table. > Triangulating a general 2D surface in 3-space is not trival since there can be > genuine ambiguity. There are programs that attempt to do it however. If I recall > correctly, some of the early molecular surface codes which generated dot surfaces > attempted triangulation in this fashion. I also recall a paper some years ago > in a SIGGRAPH journal on this subject but I can't find it at the moment. > > I'm not familiar with how cosmo cavity is defined. If it is a collection > of spheres of given radius, then you may be able to treat them like a > bunch of atoms and compute a triangulated surface using a molecular surface > algorithm. > > Good luck. > > Richard Gillilan > MacCHESS, Cornell > > > The program I've used till now, gOpenMol, is able > > to take an isosurface of a property of choice, and map another 3D-grid > > property on that, but in this case, as my surface is not defined my a > > 3D grid, this approach does not work. > > > > Any suggestions? > > > > Cheers, > > > > atte.sillanpaa@oulu.fi +358 (0)8 553 1681 (work), KE 368 > > Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) > > Po-BOX 3000 > > FIN-90014 University of Oulu > > FINLAND > > | Entropy requires no maintenance. | > > > > -= 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 -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Sep 25 02:03:51 2002 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8P63p722690 for ; Wed, 25 Sep 2002 02:03:51 -0400 Received: from [128.97.147.215] (ch-15.psnet.ucla.edu [128.97.147.215]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id g8P63nB28210 for ; Tue, 24 Sep 2002 23:03:50 -0700 (PDT) Mime-Version: 1.0 Message-Id: Date: Tue, 24 Sep 2002 23:03:28 -0700 To: ccl From: Eric Scerri Subject: Special Issue on Computational Chemistry Content-Type: multipart/alternative; boundary="============_-1179188668==_ma============" --============_-1179188668==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" Dear CCL'ers, The journal Foundations of Chemistry would like to solicit articles on foundational aspects of quantum chemistry and computational chemistry in general. Articles dealing with historical, philosophical and/or fundamental aspects will be given preference. Please take a moment to view tables of contents, instructions to authors etc. of this journal at, http://www.kluweronline.com/issn/1386-4238 Please also note that this is part of an effort to make the journal more chemical and less purely directed at philosophers/historians. Dr. Eric Scerri, UCLA, Editor of Foundations of Chemistry. --============_-1179188668==_ma============ Content-Type: text/html; charset="us-ascii" Special Issue on Computational Chemistry


Dear CCL'ers,

The journal Foundations of Chemistry would like to solicit articles on foundational aspects of quantum chemistry and computational chemistry in general.

Articles dealing with historical, philosophical and/or fundamental aspects will be given preference.

Please take a moment to view tables of contents, instructions to authors etc. of this journal at,

http://www.kluweronline.com/issn/1386-4238

Please also note that this is part of an effort to make the journal more chemical and less purely directed at philosophers/historians.


Dr. Eric Scerri,
UCLA,
Editor of Foundations of Chemistry.
--============_-1179188668==_ma============-- From chemistry-request@server.ccl.net Wed Sep 25 14:34:19 2002 Received: from umbi3.umbi.umd.edu ([136.160.7.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8PIYJa04495 for ; Wed, 25 Sep 2002 14:34:19 -0400 Received: from umbi.umd.edu ([129.6.112.53]) by umbi3.umbi.umd.edu (Netscape Messaging Server 4.15) with SMTP id H30BNY00.ECK; Wed, 25 Sep 2002 14:35:58 -0400 Message-ID: <3D920389.37D49B8C@umbi.umd.edu> Date: Wed, 25 Sep 2002 14:42:17 -0400 From: "Michael K. Gilson" Organization: CARB/UMBI X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Binding Database update Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, BindingDB now can accept on-line deposition of binding data from enzyme inhibition studies -- Ki, IC50 and the like. The current Ki holdings are all for HIV protease inhibitors, and can be viewed on-line or downloaded in the form of an SDF file. To obtain the SDF file, select the "sdf" link on the main page, www.bindingdb.org. We hope you find the site useful. Please encourage your experimentalist colleagues to deposit their calorimetry and enzyme inhibition data so that BindingDB can grow into a valuable resource for the scientific community. With best regards, Mike Gilson Center for Advanced Research in Biotechnology U. Maryland Biotechnology Institute From chemistry-request@server.ccl.net Wed Sep 25 08:41:30 2002 Received: from guppy.vub.ac.be ([134.184.129.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8PCfT729274 for ; Wed, 25 Sep 2002 08:41:30 -0400 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id OAA18887; Wed, 25 Sep 2002 14:41:24 +0200 (MET DST) for From: cbiot@ulb.ac.be Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id OAA05530; Wed, 25 Sep 2002 14:41:23 +0200 (MET DST) for Sender: christophe@mach.vub.ac.be Message-ID: <3D91AFEB.6D4171DA@ulb.ac.be> Date: Wed, 25 Sep 2002 14:45:31 +0200 Organization: ULB X-Mailer: Mozilla 4.77 [fr] (X11; U; Linux 2.4.4-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: PoPMuSiC on the web Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit PoPMuSiC is an efficient tool for rational computer-aided design of single-site mutations in proteins and peptides. Two types of queries can be submitted. The first option allows to estimate the changes in folding free energy for specific point mutations given by the user. In the second option, all possible point mutations in a given protein or protein region are performed and the most stabilizing or destabilizing mutations, or the neutral mutations with respect to thermodynamic stability, are selected. For each sequence position or secondary structure the deviation > from the most stable sequence is moreover evaluated, which helps to identify the most suitable sites for the introduction of mutations. Availability: http://babylone.ulb.ac.be/popmusic -- ******************************************************* Dr. BIOT Christophe Ingenierie Biomoleculaire, CP 165/64 Universite Libre de Bruxelles 50, Av. F. Roosevelt B-1050 Bruxelles Belgique Phone: 32-2-650 3001 Fax: 32-2-650 3606 E-mail:cbiot@ulb.ac.be http://babylone.ulb.ac.be/~christophe/ http://www.ulb.ac.be/rech/inventaire/unites/ULB163.html ******************************************************* From chemistry-request@server.ccl.net Wed Sep 25 15:19:54 2002 Received: from iss04.interliant.com ([198.3.182.194]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8PJJsa05349 for ; Wed, 25 Sep 2002 15:19:54 -0400 Received: from fsustxsmtp01.interliant.com (fsustxsmtp01.interliant.com [198.3.179.198]) by iss04.interliant.com (8.10.2/8.10.2) with ESMTP id g8PJJcm26199; Wed, 25 Sep 2002 14:19:48 -0500 (CDT) To: chemistry@ccl.net Cc: Jan Labanowski Subject: Call for Speaker and Thought Leaders for Executive Summit Focused on Drug Discovery and Development MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9 November 16, 2001 Message-ID: From: "Eric Cervera" Date: Wed, 25 Sep 2002 14:19:11 -0500 X-MIMETrack: Serialize by Router on FSUSTXSMTP01/Servers/US/Frost & Sullivan(Release 5.0.6a |January 17, 2001) at 09/25/2002 01:58:03 PM, Serialize complete at 09/25/2002 01:58:03 PM Content-Type: multipart/alternative; boundary="=_alternative 006A60D886256C3F_=" This is a multipart message in MIME format. --=_alternative 006A60D886256C3F_= Content-Type: text/plain; charset="us-ascii" Hi all, I am currently accepting nominations for the prestigious role of Thought Leader at our Executive Summit focused on: Maximizing Outcomes of Information Technology in Drug Discovery and Development. There are no presentations or speeches required. All I ask it the Though Leader share his/her insight and perspective in one of the topics listed below. Concurrent Thinktanks, November 5, 2002 __Thinktank 1: InSilico Drug Discovery __Thinktank 2: Genomics __Thinktank 3: Proteomics Concurrent Roundtables, November 6, 2002 __ Roundtable 1: Managing Focused Libraries __ Roundtable 2: E-Clinical Integration __ Roundtable 3: Personalized Medicine As a Thought Leader there are a number of exclusive privileges you will enjoy: Full Complimentary Thought Leader Pass for the Executive Forum and General Session (Sunday-Wednesday $2095 value) Your name, title and company in our program brochure and in our program materials as a participating Thought Leader Sunday's Executive Golf Tournament on us - we've got the green fees! Complimentary daily continental breakfast, lunch and scheduled receptions and dinners and more! The following is a list of confirmed Thought Leaders: Francois Nader, MD, MBA, Senior Vice President Medical Affairs, North America, Aventis Pharmaceutical Kris Arora, PhD,Vice President, GRA Information Management, Pharmacia Sheryl Torr-Brown, PhD, Worldwide Head of Knowledge Management and Scientific Development, Pfizer Sangtae Kim, PhD, Vice President and Information Officer, Lilly Research Laboratories Mark Cockett, PhD, Executive Director, Applied Genomics, Bristol-Myers Squibb Company Charles Jaffe, MD, Ph.D, Director of Medical Informatics, AstraZeneca Pharmaceuticals Abdel Laoui, Head Chemoinformatics, Lead Generation Informatics, Aventis Nigel Beeley, PhD, Vice President and Chief Chemical Officer- Arena Pharmaceuticals Daniel Marshak, PhD, VP and Chief Technology Officer- Cambrex Joe Guiles, PhD, Director of High Throughput Chemistry, Aventis Pharmaceuticals Inc. Alan Wilson, PhD, Senior Director and Senior Fellow, PreClinical Development, Pharmacia Nathan Siemers, Associate Director of Bioinformatics, Bristol-Myers Squibb Company Bob Ladner, Sr. VP & Chief Science Officer, Dyax Steven Gold, PhD, Director of Bioinformatics, CuraGen Corporation Thomas Rea, VP Bio-Pharmaceutical Development, Esperion Therapeutics Richard Labaurdiniere, PhD, Senior Vice President Research and Development, Genome Therapeutics Peter Holthe, PhD, MBA, Director, Data Managment and Clinical Systems, Roche Molecular Diagnostics, Inc. Phillip Anderson, Pharm D, University of California, San Diego Robert Davis, Executive VP of Drug Discovery, ACADIA Pharmaceuticals Lloyd Segal, President & CEO - Caprion Pharmaceuticals Jurgen Bajorath Ph.D, Senior Director, Computer Aided Drug Discovery, Albany Molecular Research Jim Rizzi, Director of Computational Technology- Array BioPharma Bruce Keyt, PhD, Vice President Preclinical Development, Abgenix Inc. Robin Jackman, VP of Corporate Development, Sequenom Terrence Chew, MD, SVP, Clinical and Regulatory, Peregrine Pharmaceutical David O'Reilly, VP of Corporate Development, Iconix Pharmaceuticals Sheila DeWitt, PhD, Vice President Drug Discovery, ArQule John Saunders, PhD, Vice President of Chemistry, Neucrine Biosciences, Inc. There are a few ground rules: 1. You must be a Director or above. 2. You must be from a Pharmaceutical or Biotechnology or Biopharma company with sales in excess of $10 million/ year. 4. Each nominee must go through a brief screening process. 5. Rules subject to change For more information about this event go to http://www.summits.frost.com Please call me at 210-355-4806 or email me at ecervera@frost.com to nominate yourself or a colleague. Best, Eric Eric Cervera Public Relations Specialist Executive Summits Division Frost & Sullivan Office # 210-247-2446 http://www.summits.frost.com --=_alternative 006A60D886256C3F_= Content-Type: text/html; charset="us-ascii"
Hi all,

 I am currently accepting nominations for the prestigious role of Thought
Leader at our Executive Summit focused on: Maximizing Outcomes of
Information Technology in Drug Discovery and Development.

There are no presentations or speeches required. All I ask it the Though
Leader share his/her insight and perspective in one of the topics listed
below.

Concurrent Thinktanks, November 5, 2002
__Thinktank 1: InSilico Drug Discovery
__Thinktank 2: Genomics
__Thinktank 3: Proteomics

Concurrent Roundtables, November 6, 2002
__ Roundtable 1: Managing Focused Libraries
__ Roundtable 2: E-Clinical Integration
__ Roundtable 3: Personalized Medicine

As a Thought Leader there are a number of exclusive privileges you will
enjoy:
Full Complimentary Thought Leader Pass for the Executive Forum and General
Session (Sunday-Wednesday $2095 value)
Your name, title and company in our program brochure and in our program
materials as a participating Thought Leader
Sunday's Executive Golf Tournament on us - we've got the green fees!
Complimentary daily continental breakfast, lunch and scheduled receptions
and dinners
and more!


The following is a list of confirmed Thought Leaders:
Francois Nader, MD, MBA, Senior Vice President Medical Affairs, North America, Aventis
Pharmaceutical
Kris Arora, PhD,Vice President, GRA Information Management, Pharmacia
Sheryl Torr-Brown,  PhD, Worldwide Head of Knowledge Management and Scientific   Development,  Pfizer
Sangtae Kim, PhD, Vice President and Information Officer, Lilly Research Laboratories
Mark Cockett, PhD, Executive Director, Applied Genomics, Bristol-Myers Squibb Company
Charles Jaffe, MD, Ph.D, Director of Medical Informatics, AstraZeneca Pharmaceuticals
Abdel Laoui, Head Chemoinformatics, Lead Generation Informatics, Aventis
Nigel Beeley, PhD, Vice President and Chief Chemical Officer- Arena Pharmaceuticals
Daniel Marshak,  PhD, VP and Chief Technology Officer- Cambrex
Joe Guiles, PhD, Director of High Throughput Chemistry, Aventis Pharmaceuticals Inc.
Alan Wilson,  PhD, Senior Director and Senior Fellow, PreClinical Development,
Pharmacia
Nathan Siemers, Associate Director of Bioinformatics, Bristol-Myers Squibb Company
Bob Ladner, Sr. VP & Chief Science Officer, Dyax
Steven Gold,  PhD,  Director of Bioinformatics, CuraGen Corporation
Thomas Rea, VP Bio-Pharmaceutical Development, Esperion Therapeutics
Richard Labaurdiniere,  PhD, Senior Vice President Research and Development, Genome Therapeutics
 Peter Holthe, PhD, MBA, Director, Data Managment and Clinical Systems, Roche Molecular Diagnostics, Inc.
 Phillip Anderson, Pharm D, University of California, San Diego
Robert Davis, Executive VP of Drug Discovery, ACADIA Pharmaceuticals
Lloyd Segal, President & CEO - Caprion Pharmaceuticals
Jurgen Bajorath Ph.D, Senior Director, Computer Aided Drug Discovery, Albany Molecular
Research
Jim Rizzi, Director of Computational Technology- Array BioPharma
Bruce Keyt,  PhD, Vice President Preclinical Development, Abgenix Inc.
Robin Jackman, VP of Corporate Development, Sequenom
Terrence Chew, MD, SVP, Clinical and Regulatory, Peregrine Pharmaceutical
David O'Reilly, VP of Corporate Development, Iconix Pharmaceuticals
Sheila DeWitt,  PhD, Vice President Drug Discovery, ArQule
John Saunders,  PhD, Vice President of Chemistry, Neucrine Biosciences, Inc.

There are a few ground rules:
1. You must be a Director or above.
2. You must be from a Pharmaceutical or Biotechnology or Biopharma company
with sales in excess of $10 million/ year.
4.  Each nominee must go through a brief screening process.
5. Rules subject to change

For more information about this event go to http://www.summits.frost.com

Please call me at 210-355-4806 or email me at ecervera@frost.com to
nominate yourself or a colleague.

Best,
Eric

Eric Cervera
Public Relations Specialist
Executive Summits Division
Frost & Sullivan
Office # 210-247-2446
http://www.summits.frost.com

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