From chemistry-request@ccl.net Thu May 5 12:34:29 2005 Received: from swip.net (mailfe07.swip.net [212.247.154.193]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j45GYKMG017370 for ; Thu, 5 May 2005 12:34:22 -0400 X-T2-Posting-ID: nmfk1yHqiShCY778n5co/A== Received: from [213.103.141.56] (HELO avdemo.tiscalinet.ch) by mailfe07.swip.net (CommuniGate Pro SMTP 4.3c5) with ESMTP id 161382268 for chemistry [a] ccl.net; Thu, 05 May 2005 18:34:14 +0200 Message-Id: <5.0.2.1.0.20050505183734.00ac2630 [a] mail.tiscalinet.ch> X-Sender: barry.hardy [a] mail.tiscalinet.ch X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Thu, 05 May 2005 18:37:39 +0200 To: chemistry [a] ccl.net From: Barry Hardy Subject: new advances in protein modelling for drug discovery Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_9628276==_.ALT" X-Spam-Status: No, score=2.0 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,HTML_10_20,HTML_MESSAGE autolearn=no version=3.0.3 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --=====================_9628276==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Activities, programs, abstracts and speaker bios of the eCheminfo Protein Interest group exploring new best practices and advances in protein modelling for drug discovery are now located at: http://echeminfo.colayer.net/COMTY_proteins Upcoming activities include a Web conference (opening May 9), and sessions at the eCheminfo Autumn InterAction meetings in Philadelphia, US (October 11-13) and Basel, Switzerland (November 8-10). Web-based conference session, May 2005 Protein Folding & Misfolding: Applications to Drug Discovery, chaired by Nikolay V. Dokholyan (University of North Carolina) and Marc Fasnacht (Columbia University) New invited seminars to be presented and discussed: Folding@Home: Using worldwide desktop grid computing to break fundamental barriers in molecular simulation,Vijay Pande (Stanford University) Design of a folding inhibitor of the HIV-1 Protease, Guido Tiana (University of Milano) Simulations of peptide inhibitors of Amyloid-beta fibrillogenesis, Joan-Emma Shea (University of California, Santa Barbara) Folding and aggregation: A physics-based all-atom modeling, Yong Duan (University of California Davis) Application of discrete molecular dynamics to protein folding and aggregation, Sergey Buldyrev (Yeshiva University) Dewetting in nanoscale hydrophobic plates collapse and multi-domain protein folding, Ruhong Zhou (IBM) Recent invited seminars available in the Proteins Interest Group area for viewing and discussion: Automated Methods for identifying Structural Motifs: Helix Couples in the Globins, Marc Fasnacht (Columbia University) Reconstructing evasive protein states using NMR and molecular modeling: the Focal Adhesion Kinase story, Nikolay V. Dokholyan (University of North Carolina) Protein modelling: simulating the thermodynamics and kinetics of protein folding, Jed Pitera (IBM) Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family, Peter Winn (EMBL, Heidelberg) Presentations will open on the eCheminfo Web site on the 9 May for a two week period of review and discussion and a conference call with the panel of presenters for Q&A on Monday, 23 May, 12.00 EDT. eCheminfo InterAction Meeting Session, Philadelphia, 12 October 2005 Protein Folding, Misfolding & Aggregation: Applications to Disease chaired by Nikolay V. Dokholyan (University of North Carolina at Chapel Hill), eCheminfo 2005 InterAction Meeting, 11-13 October 2005, Philadelphia, USA Updates loaded at http://echeminfo.colayer.net/COMTY_program Approaches to medicine are rapidly changing as we begin to comprehend human disease at the most fundamental molecular level. Much of this change is heralded by a more quantitative and mechanistic understanding of the alterations of molecular structure and dynamics that produce disease. Recent years have brought a dramatic increase in the number of known associations between human disease and abnormalities in protein dynamics and structure. In particular, the number of diseases known to be associated with protein aggregation has increased several-fold. Since protein structure and dynamics are intimately related to protein cellular function, abnormalities in protein folding dynamics and structural stability often adversely affect cell life. Understanding protein folding, misfolding and aggregation will be vital to understanding human diseases, ranging from various forms of cancer to neurodegenerative diseases, and will facilitate the development of therapeutic strategies to combat these diseases. The focus of the "Protein Folding, Misfolding & Aggregation: Applications to Disease" symposium is to bring together world-class researchers working on both theoretical and experimental fronts of the protein folding field, and have them present recent cutting-edge research results. The emphasis of the symposium is on communication and open discussion, which we hope will lead to new ideas and collaborations. eCheminfo InterAction Meeting Session, Basel, 9 November 2005 Protein Folding & Dynamics chaired by Wilfred van Gunsteren (ETH-Zurich) eCheminfo 2005 InterAction Meeting, 8-10 November 2005, Basel, Switzerland Updates loaded at http://echeminfo.colayer.net/COMTY_program After decades of largely independent experimental and theoretical work, the field of protein folding is entering a mature age in which the two are converging. Experimental techniques have become sophisticated enough to probe the folding of small, fast-folding proteins and protein elements, while computational power and algorithms have reached a level at which simulating these events is tractable. The central goal for the "Protein folding and dynamics" symposium is to bring together researchers working on both theoretical and experimental fronts of the protein folding field, and have them present recent cutting-edge research results. The emphasis of the symposium is on communication and open discussion, which we hope will lead to new ideas and collaborations. Posters All registrants for the above Protein sessions are eligible to submit a Conference Poster. Attendees may view and discuss the Posters and leave messages for the authors on the Web site. Electronic poster and discussion sessions will be scheduled to take place at both the US and European InterAction Meetings. Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted for consideration to echeminfo at douglasconnect.com Conference Posters can be presented as HTML, pdf, Powerpoint or Word documents. Access Access to all eCheminfo facilities and seminars on the website, either past or occurring at any session in 2005, including the Autumn meetings in Philadelphia and Basel, requires the completion of an eCheminfo membership through the website or by contacting Nicki Douglas (nicki.douglas [a] douglasconnect.com) Barry Hardy eCheminfo Community of Practice Manager SignUp for program updates, membership or meeting registration through the eCheminfo CoP website: http://eCheminfo.com/ eCheminfo Blog: http://barryhardy.blogs.com/cheminfostream/ Barry Hardy, PhD Douglas Connect, Switzerland +41 61 851 0170 (office) www.douglasconnect.com --=====================_9628276==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Activities, programs, abstracts and speaker bios of the eCheminfo Protein Interest group exploring new best practices and advances in protein modelling for drug discovery are now located at:
http://echeminfo.colayer.net/COMTY_proteins
Upcoming activities include a Web conference (opening May 9), and sessions at the eCheminfo Autumn InterAction meetings in Philadelphia, US (October 11-13) and Basel, Switzerland (November 8-10).

Web-based conference session, May 2005
Protein Folding & Misfolding: Applications to Drug Discovery, chaired by Nikolay V. Dokholyan (University of North Carolina) and Marc Fasnacht (Columbia University)

New invited seminars to be presented and discussed:
Folding@Home: Using worldwide desktop grid computing to break fundamental
barriers in molecular simulation,Vijay Pande (Stanford University)
Design of a folding inhibitor of the HIV-1 Protease, Guido Tiana (University of Milano)
Simulations of peptide inhibitors of Amyloid-beta fibrillogenesis, Joan-Emma Shea (University of California, Santa Barbara)
Folding and aggregation: A physics-based all-atom modeling, Yong Duan (University of California Davis)
Application of discrete molecular dynamics to protein folding and aggregation, Sergey Buldyrev (Yeshiva University)
Dewetting in nanoscale hydrophobic plates collapse and multi-domain protein folding, Ruhong Zhou (IBM)

Recent invited seminars available in the Proteins Interest Group area for viewing and discussion:
Automated Methods for identifying Structural Motifs: Helix Couples in the Globins, Marc Fasnacht (Columbia University)
Reconstructing evasive protein states using NMR and molecular modeling: the Focal Adhesion Kinase story, Nikolay V. Dokholyan (University of North Carolina)
Protein modelling: simulating the thermodynamics and kinetics of protein folding, Jed Pitera (IBM)
Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family, Peter Winn (EMBL, Heidelberg)

Presentations will open on the eCheminfo Web site on the 9 May for a two week period of review and discussion and a conference call with the panel of presenters for Q&A on Monday, 23 May, 12.00 EDT.

eCheminfo InterAction Meeting Session, Philadelphia, 12 October 2005
Protein Folding, Misfolding & Aggregation: Applications to Disease
chaired by Nikolay V. Dokholyan (University of North Carolina at Chapel Hill),
eCheminfo 2005 InterAction Meeting, 11-13 October 2005, Philadelphia, USA
Updates loaded at http://echeminfo.colayer.net/COMTY_program

Approaches to medicine are rapidly changing as we begin to comprehend human disease at the most fundamental molecular level. Much of this change is heralded by a more quantitative and mechanistic understanding of the alterations of molecular structure and dynamics that produce disease. Recent years have brought a dramatic increase in the number of known associations between human disease and abnormalities in protein dynamics and structure. In particular, the number of diseases known to be associated with protein aggregation has increased several-fold. Since protein structure and dynamics are intimately related to protein cellular function, abnormalities in protein folding dynamics and structural stability often adversely affect cell life. Understanding protein folding, misfolding and aggregation will be vital to understanding human diseases, ranging from various forms of cancer to neurodegenerative diseases, and will facilitate the development of therapeutic strategies to combat these diseases.

The focus of the "Protein Folding, Misfolding & Aggregation: Applications to Disease" symposium is to bring together world-class researchers working on both theoretical and experimental fronts of the protein folding field, and have them present recent cutting-edge research results. The emphasis of the symposium is on communication and open discussion, which we hope will lead to new ideas and collaborations.

eCheminfo InterAction Meeting Session, Basel, 9 November 2005
Protein Folding & Dynamics
chaired by Wilfred van Gunsteren (ETH-Zurich)
eCheminfo 2005 InterAction Meeting, 8-10 November 2005, Basel, Switzerland
Updates loaded at http://echeminfo.colayer.net/COMTY_program

After decades of largely independent experimental and theoretical work, the field of protein folding is entering a mature age in which the two are converging. Experimental techniques have become sophisticated enough to probe the folding of small, fast-folding proteins and protein elements, while computational power and algorithms have reached a level at which simulating these events is tractable. The central goal for the "Protein folding and dynamics" symposium is to bring together researchers working on both theoretical and experimental fronts of the protein folding field, and have them present recent cutting-edge research results. The emphasis of the symposium is on communication and open discussion, which we hope will lead to new ideas and collaborations.

Posters
All registrants for the above Protein sessions are eligible to submit a Conference Poster. Attendees may view and discuss the Posters and leave messages for the authors on the Web site. Electronic poster and discussion sessions will be scheduled to take place at both the US and European InterAction Meetings.

Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted for consideration to echeminfo at douglasconnect.com Conference Posters can be presented as HTML, pdf, Powerpoint or Word documents.

Access
Access to all eCheminfo facilities and seminars on the website, either past or occurring at any session in 2005, including the Autumn meetings in Philadelphia and Basel, requires the completion of an eCheminfo membership through the website or by contacting Nicki Douglas (nicki.douglas [a] douglasconnect.com)


Barry Hardy
eCheminfo Community of Practice Manager

SignUp for program updates, membership or meeting registration through the eCheminfo CoP website: http://eCheminfo.com/
eCheminfo Blog: http://barryhardy.blogs.com/cheminfostream/


Barry Hardy, PhD
Douglas Connect, Switzerland
+41 61 851 0170 (office)
www.douglasconnect.com
 --=====================_9628276==_.ALT-- From chemistry-request@ccl.net Thu May 5 14:03:45 2005 Received: from out-mail03.yourhostingaccount.com (outmail.yourhostingaccount.com [65.254.254.71]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j45I3bAf024137 for ; Thu, 5 May 2005 14:03:38 -0400 Message-Id: <200505051803.j45I3bAf024137*&*server.ccl.net> Received: from scan04.yourhostingaccount.com ([10.1.1.234] helo=scan04.yourhostingaccount.com) by mail03.yourhostingaccount.com with esmtp (Exim) id 1DTjNq-0008Eu-Tw for chemistry*&*ccl.net; Thu, 05 May 2005 12:39:30 -0400 Received: from authsmtp02.yourhostingaccount.com ([10.1.1.156] ident=exim) by scan04.yourhostingaccount.com with spamscanlookuphost (Exim) id 1DTjNr-0000iI-DP for chemistry*&*ccl.net; Thu, 05 May 2005 12:39:31 -0400 Received: from authsmtp02.yourhostingaccount.com ([10.1.1.156] helo=authsmtp02.yourhostingaccount.com) by scan04.yourhostingaccount.com with esmtp (Exim) id 1DTjNr-0000iF-5N for chemistry*&*ccl.net; Thu, 05 May 2005 12:39:31 -0400 Received: from adsl-64-166-142-98.dsl.snfc21.pacbell.net ([64.166.142.98] helo=Hummer) by authsmtp02.yourhostingaccount.com with esmtpa (Exim) id 1DTjNq-0007qi-6f for chemistry*&*ccl.net; Thu, 05 May 2005 12:39:30 -0400 From: "Warren DeLano" To: Subject: PyMOL 0.98 Released Date: Thu, 5 May 2005 09:39:25 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 Thread-Index: AcVRkP7tiyHLjSdPTqCQki1BBZt3kg== X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-EN-UserInfo: dfab58b57aa3bb910bf055c23b06c5c7:c10f421fef69a2b5fe207cfa50def74f X-EN-AuthUser: warren_1 Sender: "Warren DeLano" X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net CCL: PyMOL 0.98 has been released. If you haven't tried PyMOL in the past year, please give it a shot. It runs on every major platform, and there is a 700-user strong mailing list based around it, as well as a user-managed Wiki. Download: http://delsci.com/rel/0_98 Homepage: http://www.pymol.org For a quick look at what PyMOL can do for your molecular graphics, check out the F-type ATPase structures in the latest issue of Science. http://www.sciencemag.org/content/vol308/issue5722/cover.shtml Commercial disclaimer: Though the PyMOL source code is free and open-source, DeLano Scientific LLC does ask you to sponsor the project if you rely upon our convenient PyMOL Executable Builds beyond a "finite honor-sytem evaluation period". What that phrase means exactly is up to you... Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren*&*delsci.com From chemistry-request@ccl.net Thu May 5 15:46:48 2005 Received: from cmbi2.cmbi.ru.nl (cmbi2.cmbi.ru.nl [131.174.88.32]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j45Jkggp003374 for ; Thu, 5 May 2005 15:46:43 -0400 Received: from cmbi6.cmbi.ru.nl (cmbi6.cmbi.ru.nl [131.174.88.36]) by cmbi2.cmbi.ru.nl (8.12.10/8.12.10) with ESMTP id j45IitwC007110 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO); Thu, 5 May 2005 20:44:55 +0200 Date: Thu, 5 May 2005 20:44:54 +0200 (CEST) From: Gijs Schaftenaar To: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= cc: CCL posting Subject: Re: CCL:Viewing diffuse orbitals In-Reply-To: <4278DD06.2090302|at|up.univ-mrs.fr> Message-ID: References: <4278DD06.2090302|at|up.univ-mrs.fr> MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-1367137192-816883802-1115318694=:22020" X-CMBI-MailScanner-Information: Please contact the ISP for more information X-CMBI-MailScanner: Found to be clean X-CMBI-MailScanner-SpamCheck: not spam (whitelisted), SpamAssassin (score=-2.571, required 6, autolearn=not spam, AWL 0.03, BAYES_00 -2.60) X-MailScanner-From: schaft|at|cmbi.ru.nl X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---1367137192-816883802-1115318694=:22020 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE Dear Nicolas Ferre, What i would do, is calculate the electron density on a 3D grid with a basis-set including the diffuse functions and a basis set without. Then look at the difference density between both. This is all possible with molden (see section Basisset Differ., buttons "Write Grid", "Read Grid" -> subtract). Best Regards, Gijs Schaftenaar Author of Molden +----------------------------+-----------------------------------+ Gijs Schaftenaar, Dr. | CMBI Email: schaft|at|cmbi.ru.nl | Radboud University of Nijmegen URL : http://www.cmbi.ru.nl/staff/schaft.html Tel. : +31 24 3653388 | Toernooiveld 1 Fax : +31 24 3652977 | 6525 ED Nijmegen, The Netherlands +----------------------------------------------------------------+ On Wed, 4 May 2005, [ISO-8859-1] Nicolas Ferr=E9 wrote: > Date: Wed, 04 May 2005 16:32:38 +0200 > From: "[ISO-8859-1] Nicolas Ferr=E9" > To: CCL posting > Subject: CCL:Viewing diffuse orbitals >=20 > Dear ccl, > > I am looking for an orbital viewer, with special interest on very diffuse= =20 > functions, actually Rydberg-type orbitals obtained from a molcas job. I j= ust=20 > tried molden, without luck. Maybe I am missing a trick with molden, but I= =20 > don't believe that there exists a zoom in molden's orbital mode. > > > --=20 > *********** Dr. Nicolas Ferre' *********** > Laboratoire de Chimie Theorique et de Modelisation Moleculaire > UMR 6517 - CNRS Universites Aix-Marseille Case 521 > Centre de Saint-Jerome 13397 - Marseille Cedex 20, France > Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58 > http://www.up.univ-mrs.fr/wsrep/ctheo/lctmm.html > *************************************************************** > > > -=3D This is automatically added to each message by the mailing script = =3D- > To send e-mail to subscribers of CCL put the string CCL: on your Subject:= =20 > line > and send your message to: CHEMISTRY|at|ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST@ccl.= net=20 > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs=20 > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page=20 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > ---1367137192-816883802-1115318694=:22020--