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elNémo is the Web-interface to the Elastic Network Model (ENM),
a fast and simple way for computing the low frequency normal modes of a macromolecule
(Tirion, 1996). Note that, thanks to the RTB approximation
(Durand et al., 1994; Tama et al., 2000), this server
can perform calculations for all-atom systems.
One major application of normal modes
is the identification of potential conformational changes
(Tama and Sanejouand, 2001; Delarue and Sanejouand, 2002),
e.g. of enzymes upon ligand binding. It has for instance been used
in the study of membrane channel opening
(Valadie et al., 2003)
and for the analysis of structural movements of systems as large as the ribosome
(Tama et al., 2003).
It has been shown that in 50% of the cases where protein structures are
available in two different conformations, the related movement
can be described by using only one or two low frequency normal modes
(Krebs et al., 2002).
This prompts for an application in X-ray cristallography data phasing, that is to use
normal mode perturbed models as templates in molecular replacement
(Suhre and Sanejouand, 2004).
Some applications of normal mode analysis are presented
in the example section.
In the reference section you may find a number
of papers that describe the concepts behind this approach.
To access previous jobs, go to the job status page.
The present version of elNémo allows you to compute
the low frequency normal modes for a given protein structure in PDB format.
You will be able to analyse these modes at different levels of detail, i.e.
compare the collectivity of the modes, view 3-D animations of the protein
movement for each mode and identify those residues that have the largest distance fluctuations
in a given mode.
Comparision of B-factors derived from the normal mode decomposition and
measured B-factors gives an indication on differences in protein flexibility of the free
protein and the protein in a crystallographic environment.
When you submit two conformations of the same protein, you may analyse
the contribution of each mode to the conformational changes
(overlap between a protein motion and a normal mode).
When two homologous proteins are submitted, the root mean square distance (RMSD) between
all residues and the number of residues that are closer than 3A
as a function of mode and perturbation can be computed.
Perturbed structures in PDB format can be downloaded for use as templates in molecular replacement.
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