From chemistry-request@server.ccl.net Sun Aug 1 02:39:06 1999 Received: from fred.interval.com (fred.interval.com [192.203.7.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA02674 for ; Sun, 1 Aug 1999 02:39:05 -0400 Received: from interval.interval.com (interval.interval.com [199.170.107.10]) by fred.interval.com with ESMTP id XAA04863; Sat, 31 Jul 1999 23:33:24 -0700 (PDT) Received: by interval.interval.com id XAA29934; Sat, 31 Jul 1999 23:33:23 -0700 (PDT) Received: by harp.interval.com with Internet Mail Service (5.5.2448.0) id ; Sat, 31 Jul 1999 23:33:20 -0700 Message-ID: <4910A1687590D21190050008C7B1E9F42E1FCC@harp.interval.com> From: Tom Ngo To: "'JATI KASTANJA'" Cc: "'chemistry@ccl.net'" Subject: RE: Levinthal's paradox Date: Sat, 31 Jul 1999 23:33:15 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Jati, Also relevant to your inquiry are the references below. We argue in the first paper that the astronomical number of conformational states does not, by itself, give reason to conclude that folding should take exponential time. We show how the theory of NP-completeness can be brought to bear on questions related to folding times. * J. Thomas Ngo, Joe Marks and Martin Karplus, "Computational Complexity, Protein Structure Prediction, and the Levinthal Paradox," in The Protein Folding Problem and Tertiary Structure Prediction, Kenneth Merz, Jr. and Scott LeGrand, eds., pp. 433-506, Birkhauser, Boston, 1994. * J. Thomas Ngo and Joe Marks, "Computational Complexity of a Problem in Molecular Structure Prediction," Protein Engineering 5(4):313-321, June 1992. --Tom Ngo > -----Original Message----- > From: JATI KASTANJA [mailto:jkastanja@dwi.rwth-aachen.de] > Sent: Friday, July 30, 1999 10:53 AM > To: chemistry@ccl.net > Subject: CCL:Levinthal's paradox > > > Dear CCLers, > does anyone know something about the Levinthal paradox? > It deals with the fact that proteins do fold into unique states in > seconds. Considering the number of all possible conformations it > seems to be quite impossible to do the fold in such a short time. > Until now I am unsuccessful in finding out the journal where Cyrus > Levinthal first published something about this paradox. > I would be very glad to get any advice. Thanks in advance. > > Regards, Jati From chemistry-request@server.ccl.net Sun Aug 1 23:50:35 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA10440 for ; Sun, 1 Aug 1999 23:50:35 -0400 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id XAA05575 for ; Sun, 1 Aug 1999 23:45:28 -0400 (EDT) Date: Sun, 1 Aug 1999 23:45:28 -0400 (EDT) From: Iraj Daizadeh To: chemistry@ccl.net Subject: Re: CCL:Large matrix diagonalization. In-Reply-To: <37A1408F.832CC2F@inorg.chem.ethz.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Cool down with the soap box garbage...it is simply unwarranted in this case (as in most --it not ALL--cases)...obviously cboris was used for a variety of reasons--our calculations stemmed from a sort of ext. huckel calculation,etc......and as to the comment on lapack stuff...we note that for the matrices we were interested in -- which you have no idea how sparse they were nor, on a more trivial note, even what general form the matrices were in (complex/real)--positive definite, etc...!--...dsygv, for example -- was later found to be quite effective for our calculations.the routine that we used was also optimized on the machine we were running on...The details of my email admittedly were poorly worded...but such generalizations produced from some members of the CCL audience that dealt with the scientific merit of utilizing one routine over another is simply non-sensical and COMPLETELY UNWARRENTED! iraj...