From chemistry-request@server.ccl.net Sun Feb 6 19:18:15 2000 Received: from smtp3.fas.harvard.edu (smtp3.fas.harvard.edu [140.247.30.83]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA26550 for ; Sun, 6 Feb 2000 19:18:15 -0500 Received: from is06.fas.harvard.edu (IDENT:daizadeh@is06.fas.harvard.edu [140.247.30.106]) by smtp3.fas.harvard.edu with ESMTP id SAA14566 Received: by is06.fas.harvard.edu with ESMTP id SAA01977 Date: Sun, 6 Feb 2000 18:09:53 -0500 (EST) From: Iraj Daizadeh To: pdb-l@rcsb.org cc: chemistry@ccl.net Subject: finding water in cavities. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Gert Vriend from the embl had a very good point. The question should be: What programs are currently available determine ``where waters sit in macromolecules, or, if there are no waters in the PDB file, finding the cavities that are large enough to hold [water].'' Any thoughts? Programs or advice on this question would be appreciated. Iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories, Box #140 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@fas.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh From chemistry-request@server.ccl.net Sun Feb 6 19:37:31 2000 Received: from efriedman.biomath.nyu.edu (EFRIEDMAN.BIOMATH.NYU.EDU [128.122.250.118]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA26647 for ; Sun, 6 Feb 2000 19:37:31 -0500 Received: from localhost (strahs@localhost) by efriedman.biomath.nyu.edu (8.9.3/8.9.3) with ESMTP id SAA532815; Sun, 6 Feb 2000 18:30:15 -0500 (EST) Date: Sun, 6 Feb 2000 18:30:15 -0500 From: Dan Strahs To: Iraj Daizadeh cc: Mihaly Mezei , pdb-l@rcsb.org, chemistry@ccl.net Subject: Re: CCL:finding water in cavities. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I suggest the following reference on the uses of GCMC: Guarnieri, F., and Mezei, M. (1996) Simulated Annealing of the Chemical Potential: A General Procedure for Locating Bound Waters. Application to the Study of the Differential Hydration Propensities of the Major and Minor Groove of DNA. J. Am. Chem. Soc., 118:8493-8494 The method has also been applied to proteins (notably BPTI, to analytically determine the 4 known internal waters). I'm not clear if they published this study, though. You can contact Mihaly Mezei @ mezei@Inka.MSSM.EDU. Dan Strahs On Sun, 6 Feb 2000, Iraj Daizadeh wrote: > > > Gert Vriend from the embl had a very good point. > > The question should be: > > > What programs are currently available determine ``where waters sit in > macromolecules, or, if there are no waters in the PDB file, finding the > cavities that are large enough to hold [water].'' > > > Any thoughts? Programs or advice on this question would be appreciated. > > Iraj. > > > Iraj Daizadeh, Ph.D. > Harvard University > Department of Cellular and Molecular Biology > The Biological Laboratories, Box #140 > 16 Divinity Avenue > Cambridge, MA 02138 > Phone: (617) 495-0783 > (617) 495-0560 > Fax: (617) 496-4313 > Email: daizadeh@fas.harvard.edu > WebPage: http://mcb.harvard.edu/gilbert/daizadeh > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >