elNémo is the Web-interface to The Elastic Network Model, a fast and simple tool to compute the low frequency normal modes of a protein.

One major application of normal modes is the identification of potential conformational changes, e.g. of enzymes upon ligand binding. It has also been used recently in the study of membrane channel opening and the analysis of structural movements of the ribosome.

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. Comparison 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.