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.
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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
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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.
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