From owner-chemistry@ccl.net Sat Feb 24 00:31:00 2007 From: "Juan C. Drosos jdrosos ~ gmail.com" To: CCL Subject: CCL: about dms.shar Message-Id: <-33696-070222175105-8605-8iWIn9GjK2VVoOwz1gmQxQ[]server.ccl.net> X-Original-From: "Juan C. Drosos" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Feb 2007 17:10:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Juan C. Drosos" [jdrosos#,#gmail.com] Does any of you out there know where to find the dms.shar source code (molecular surface) because the link at ftp.cgl.ucsf.edu seems to be broken thanks in advance From owner-chemistry@ccl.net Sat Feb 24 10:54:01 2007 From: "Forlani Roberto roberto.forlani : nikemresearch.com" To: CCL Subject: CCL: Docking programs Message-Id: <-33697-070223111305-29225-il5EBQOqVw1sT4HuppQ+RQ%x%server.ccl.net> X-Original-From: "Forlani Roberto" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 23 Feb 2007 16:40:30 +0100 MIME-Version: 1.0 Sent to CCL by: "Forlani Roberto" [roberto.forlani===nikemresearch.com] > -----Original Message----- > From: owner-chemistry[]ccl.net [mailto:owner-chemistry[]ccl.net] > Sent: Friday, February 23, 2007 12:50 AM > To: Forlani Roberto > Subject: CCL: Docking programs > > > > Sent to CCL by: "Ronald L Cook" [cookrl###tda.com] > Dear CCLers > > Many of the docking programs available calculate a fit > between a host (e.g. an enzyme, etc) and a small molecule to > look for small molecule drugs. My interest/need lies in the > opposite direction. Does anyone know of a program that takes > a guest and (using for example a genetic algorithm or other > equivalent stochastic optimization method) builds a small > peptide (or other molecular backbone) chain that provides a > good fit to the small molecule? > > Thanks > Ronald Cook > Principal Scientist > TDA Research, Inc. > Ronald, I think you should give a look at the following publication: http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/asap/abs/ci600233v.html ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands Wei Chen and Michael K. Gilson* Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850 Received June 12, 2006 Abstract: Low-molecular-weight receptors that bind targeted guest molecules have a wide range of potential applications but are difficult to design. This paper describes an evolutionary method for computer-aided design of such receptors that works by linking together chemical components from a user-defined library around a stable conformation of the targeted ligand. The software can operate in three modes: de novo design, in which it builds a wide variety of receptors from small components; macrocycle design, in which it builds homopolymeric macrocycles around the ligand; and elaboration of an existing receptor structure. The top candidates generated by the automatic construction process are further studied with detailed affinity calculations whose validity is supported by prior studies of experimentally characterized host-guest systems. All three modes of operation are illustrated here through the design of novel adenine receptors. HTH, Roberto From owner-chemistry@ccl.net Sat Feb 24 12:58:00 2007 From: "Elaine Meng meng^cgl.ucsf.edu" To: CCL Subject: CCL: about dms.shar Message-Id: <-33698-070224125524-1532-VB1IWMwKp9CaTN+XfQazMg.:.server.ccl.net> X-Original-From: "Elaine Meng" Date: Sat, 24 Feb 2007 12:55:21 -0500 Sent to CCL by: "Elaine Meng" [meng(-)cgl.ucsf.edu] Hi Juan, The description of DMS is here: http://www.cgl.ucsf.edu/Overview/software.html which links to the shar file here: ftp://ftp.cgl.ucsf.edu/pub/dms.shar Both of these links work for me today - if you still have trouble, let us (me) know. Best, Elaine ----- Elaine C. Meng, Ph.D. meng__cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Sat Feb 24 17:12:00 2007 From: "Alex Allardyce aa]*[chemaxon.com" To: CCL Subject: CCL: First call for papers: ChemAxon's 2007 User Group Meeting and Training Day, June 13-14 and June 12, Budapest, Hungary Message-Id: <-33699-070224165957-5748-RsUCIPoDAgb6kyAJv6+kWw+/-server.ccl.net> X-Original-From: Alex Allardyce Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 24 Feb 2007 16:59:44 -0500 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa=chemaxon.com] CORRECTION ChemAxon's 2007 User Group Meeting will be held on Wednesday and Thursday, June 13-14 at the Gellert Hotel Spa in Budapest, Hungary. The meeting will preceded by a training day on June 12. Apologies for misdirection Alex Alex Allardyce aa-#-chemaxon.com wrote: > > Sent to CCL by: Alex Allardyce [aa() chemaxon.com] > Hi > > ChemAxon's 2007 User Group Meeting will be held on Wednesday and > Thursday, June 12-13 at the Gellert Hotel Spa in Budapest, Hungary. > The meeting will preceded by a training day on June 12. *NO. June 13-14* > > The User Group Meeting will feature oral and poster presentations from > ChemAxon users, scientists and developers as well as several social > events to mix and speak with staff and peers. > We are inviting those interested in presenting at the meeting to > submit abstracts for review. The deadline for receipt of oral > abstracts is March 26th and June 1st for poster abstracts. To find out > more and submit your abstract please visit: > http://www.chemaxon.com/UGM/07/index.html > > The training day will give hands on experience with ChemAxon end user > applications to take attendees through common tasks in the discovery > and optimization process. Closing the training day we will have an > open session "Live FAQ" for all meeting attendees. > > We hope you can participate in what has proven to be a most > interesting and enjoyable cheminformatics event. > > See you there. > > Alex -- Alex Allardyce Dir. Marketing, ChemAxon Cell-US: 1-857-544-0541 skype: alex_allardyce From owner-chemistry@ccl.net Sat Feb 24 21:51:01 2007 From: "dave.winkler__csiro.au" To: CCL Subject: CCL: Data on CO2 sequestration by amines Message-Id: <-33700-070224214719-21885-1UidyRA/sBPQoQmJHSzGeA(a)server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Sun, 25 Feb 2007 13:12:08 +1100 MIME-Version: 1.0 Sent to CCL by: [dave.winkler:csiro.au] Does anyone know where I could find some quantitative data on the reaction of organic bases (amines are most commonly used) with CO2. Equilibrium constants, association constants and the like would be very useful, with as much molecular diversity as possible. I can't find much in the literature and, obvious sources like J Chem Info Ref Data, seem to be silent on this. Any help would be greatly appreciated. Dave Winkler