AMBER Archive (2004)

Subject: AMBER: announcing normal mode analysis web server ElNemo

From: Karsten Suhre (
Date: Thu Jul 15 2004 - 03:21:07 CDT

Dear Amber users,

although not directly linked to Amber, I thought that some of you might be
interested in our new protein normal mode analysis web-server ElNemo. A
particular interesting application of normal modes in the context of
molecular dynamics modelling is the possibility to generate initial models
with very different conformations as compared to available PDB structures.

ElNemo is available at:

A paper describing its functions has just been published in the NAR web-server
issue: (This paper is
open access)

I hope that you will find this web server useful and I would be happy about
comments or suggestions,

Kind regards, Karsten.


ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

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

-- Karsten Suhre Charge de Recherche CNRS (Research Scientist) Information Genomique & Structurale UPR CNRS 2589 31, chemin Joseph Aiguier F-13402 Marseille Cedex 20 Tel: ++ Sec: ++ Fax: ++

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