From owner-bionews@hgmp.mrc.ac.uk Sun Sep 26 18:44:14 2004 Return-Path: X-Original-To: bionews-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 0B4F07D0C9 for ; Sun, 26 Sep 2004 18:44:14 +0100 (BST) X-Original-To: bionews-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 962047D0F1 for ; Sun, 26 Sep 2004 18:44:13 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6022) id 3EECE7D0C9; Sun, 26 Sep 2004 18:44:11 +0100 (BST) X-Original-To: bionet-announce@net.bio.net Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DA4B97D115 for ; Thu, 23 Sep 2004 08:55:38 +0100 (BST) Received: from horus.isnic.is (horus.isnic.is [193.4.58.12]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AE5D57D0E2 for ; Thu, 23 Sep 2004 08:55:30 +0100 (BST) Received: from proxy.google.com (proxy.google.com [216.239.37.5]) by horus.isnic.is (8.12.9p2/8.12.9/isnic) with ESMTP id i8N7fwmC076768 for ; Thu, 23 Sep 2004 07:41:58 GMT (envelope-from news@google.com) Received: from G000080 by proxy.google.com with ESMTP id i8N7frAX005408 for ; Thu, 23 Sep 2004 00:41:53 -0700 Received: (from news@localhost) by Google Production with id i8N7frAL021059 for bionet-announce@moderators.isc.org; Thu, 23 Sep 2004 00:41:53 -0700 To: bionet-announce@moderators.isc.org From: karsten_suhre@yahoo.fr (Karsten) Newsgroups: bionet.announce Subject: announcing normal mode analysis web server ElNemo Organization: http://groups.google.com Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: posting.google.com 1095925313 21058 127.0.0.1 (23 Sep 2004 07:41:53 GMT) X-Complaints-To: groups-abuse@google.com NNTP-Posting-Date: Thu, 23 Sep 2004 07:41:53 +0000 (UTC) Date: Sun, 26 Sep 2004 18:44:11 +0100 (BST) Sender: owner-bionews@hgmp.mrc.ac.uk Precedence: bulk I am pleased to announce our new protein normal mode analysis web-server ElNemo: http://igs-server.cnrs-mrs.fr/elnemo/ A paper describing its functions has just been published in the NAR web-server issue (see abstract below): http://nar.oupjournals.org/cgi/content/full/32/suppl_2/W610 (This paper is open access) I hope that you will find this web server useful and would begrateful for any comments or suggestions, Kind regards, Karsten. ---- Karsten Suhre and Yves-Henri Sanejouand ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Nucleic Acids Research, 32, W610-W614, 2004. ABSTRACT -------- Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the ‘rotation-translation-block' (RTB) approximation implemented in ElNémo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html. .