AMBER: announcing normal mode analysis web server ElNemo

From: Karsten Suhre <Karsten.Suhre.igs.cnrs-mrs.fr>
Date: Thu, 15 Jul 2004 10:21:07 +0200

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:

http://igs-server.cnrs-mrs.fr/elnemo/

A paper describing its functions has just been published in the NAR web-server
issue:

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 I would be happy about
any
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 
http://igs-server.cnrs-mrs.fr/elnemo/index.html.
-- 
Karsten Suhre                  
Charge de Recherche CNRS (Research Scientist)  
Information Genomique & Structurale       
UPR CNRS 2589
31, chemin Joseph Aiguier            
F-13402 Marseille Cedex 20
Tel: ++33.4.91.16.46.04             
Sec: ++33.4.91.16.45.48             
Fax: ++33.4.91.16.45.49             
mailto:Karsten.Suhre.igs.cnrs-mrs.fr      
http://igs-server.cnrs-mrs.fr/~suhre
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Received on Thu Jul 15 2004 - 09:53:00 PDT