From bryant@melanie Mon Nov 4 13:07:42 1996 Return-Path: Received: from ray.nlm.nih.gov by frodo.nlm.nih.gov id NAA07796; Mon, 4 Nov 1996 13:07:41 -0500 Received: from melanie.nlm.nih.gov by ray.nlm.nih.gov id NAA01316; Mon, 4 Nov 1996 13:01:44 -0500 Received: by melanie.nlm.nih.gov (951211.SGI.8.6.12.PATCH1042/5.6) id NAA12970; Mon, 4 Nov 1996 13:01:42 -0500 From: "Stephen Bryant" Message-Id: <9611041301.ZM12968@melanie> Date: Mon, 4 Nov 1996 13:01:42 -0500 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: anjum@sunder.niddk.nih.gov, michael@iris3.carb.nist.gov, baxevanis@ncbi.nlm.nih.gov, brbrooks@helix.nih.gov, bryant@ncbi.nlm.nih.gov, burt@fcrfv3.ncifcrf.gov, lcao@helix.nih.gov, susan@vger.niddk.nih.gov, chan@sunder.niddk.nih.gov, chantal@vger.niddk.nih.gov, chatfiel@helix.nih.gov, covell@ncifcrf.gov, sun@vger.niddk.nih.gov, drd@vger.niddk.nih.gov, fmd@d4.niaid.nih.gov, valedf@helix.nih.gov, dyda@vger.niddk.nih.gov, wae@nihcu.bitnet, sle@vger.niddk.nih.gov, ericksonj@fcrfv1.ncifcrf.gov, richard_feldmann@nihdcrt.bitnet, kaf@iris5.carb.nist.gov, guy@fcrfv1.ncifcrf.gov, bhardy@helix.nih.gov, milan@helix.nih.gov, hu@sunder.niddk.nih.gov, hurley@vger.niddk.nih.gov, gah@helix.nih.gov, cch@vger.niddk.nih.gov, jernigan@fcrfv1.ncifcrf.gov, jiang@fcrfv1.ncifcrf.gov, shj@helix.nih.gov, nla@helix.nih.gov, SHUYUN@FCRFV2.NCIFCRF.GOV, bkl@helix.nih.gov, shuo@fcrfv2.ncifcrf.gov, lustig@lustig.nci.nih.gov, madan@helix.nih.gov, jmaizel@fcrfv1.ncifcrf.gov, David_Margulies@d10.niaid.pc.niaid.nih.gov, michaels@helix.nih.gov, miyazawa@lmmbsparc.nci.nih.gov, jmoult@iris4.carb.nist.gov, munson@helix.nih.gov, ruthn@fcrfv1.ncifcrf.gov, eap@vger.niddk.nih.gov, vap@nihcu.bitnet, rpearls@helix.nih.gov, prabhu@count.nlm.nih.gov, ptitsyn@lmmb.nci.nih.gov, raghu@fcrfv1.ncifcrf.gov, rodbard@nihdcrt.bitnet, sergeev@helix.nih.gov, rich@brb.nci.nih.gov, steinbac@helix.nih.gov, peter@iris3.carb.nist.gov, rtaylor@sun_of_spock.dcrt.nih.gov, dave@folding2.umd.edu, ting@fcrfv1.ncifcrf.gov, tsai@fcrfv1.ncifcrf.gov, ron@iris1.carb.nist.gov, zhang@helix.nih.gov, zhon@helix.nih.gov, zhurkin@fcrfv1.ncifcrf.gov, ncbi-seminar@melanie Subject: Seminar Friday Nov. 8 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Length: 1956 X-IMAPbase: 1000759403 1 Status: O X-Status: X-Keywords: X-UID: 1 Dear All, We have a special visitor this friday, John Gunn from the University of Montreal. He will describe some of his recent work in simulation of protein folding. His talk will be at 2pm, Friday, Nov. 8, in the NCBI conference room, 8th floor, building 38A. Don't miss this one! Steve Modeling Protein Folding with the Hierarchical Algorithm New methods will be discussed which efficiently sample the possible compact structures of reduced-model proteins and which address the combinatorical problem of minimizing a global energy function with a large number of degrees of freedom. The model representation consists of a series of residues, each having a discrete set of conformational states, which is divided into segments of assigned secondary structure. Mutations are introduced by replacing single loop segments, or pairs of loops including the intervening helix or strand, from lists of precalculated segments which are modified in turn using pre-screened libraries of randomly-generated three-residue segments. The genetic algorithm consists of growth cycles in which new combinations of existing loops are added to the ensemble, mutation cycles, and selection cycles in which a subset of structures are passed on to the next generation. The potential function consists of an empirical table-lookup contact energy, and it is evaluated using a hierarchical screening method. At each of four levels of resolution, an approximate energy is calculated and those trial structures which do not meet a cutoff value are rejected without passing to the more detailed functions. The performance of the algorithm is studied using three model potential functions and a set of test proteins ranging in size from 60 to 193 residues. John Gunn (gunnj@cerca.umontreal.ca) | "Et des boyaux du dernier pretre, Departement de Chimie / CERCA | serrons le cou du dernier roi." Universite de Montreal | -Denis Diderot