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Elastic energy plots of Normal Modes: kinetically hot residues

For each specified mode, we deform each residue along the normal mode with a small amplitude and calculate the resulting change in elastic energy.
Those residues with a high score are kinetically hot and deserve further characterization.
This is equivalent (see PNAS 2006 103:7664-9 here) to the perturbation analysis of W. Zheng, B.R. Brooks, S. Doniach, D. Thirumalai (Structure, 2005, 13, 565-577; see Ref here).

This version of the program works on CA-only PDB input files and uses Y.-H. Sanejouand's code.

Output files are PDB files (elastic_energy_###.pdb), one per mode, containing, for each residue, the delta_omega (last colum i.e. B-factors) and the rmsd (one before last column). This allows easy visualisation by B-factors coloring in Pymol. The files are tar-red in a single file to save space.

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters)

PDB file to calculate modes for
(Example: 1GGG_ca.pdb):

Number of modes to calculate
(max 106 to save our disk):

(The first six are translation and rotation.)

ENM Cutoff to use for mode calculation (Ångström):

Input data formats

  • The job title is just for your own identification, but note that it will show up in the public job queue (but your results will not be public).

  • The coordinate file should be in PDB format, with only a single structure (no multiple models). Atoms marked with alternate residue flags will be removed. Whatever atoms are in the file will be used for the calculation. The length of each mode vector will be 3*natoms. It is better not to include Hydrogen atoms in the PDB file.

  • A cutoff is used in the mode calculation. In the Tirion model (Elastic Network Model) only those pairs of atoms that are closer than the cutoff are linked by a spring of universal length. Ideally this should be choosen so that the weighting causes the interactions to be negligible outside the cutoff, but in practice a cutoff around 10 Angstrom works fine in almost all cases. In general you might be able to use a smaller cutoff value for all-atom calculations than CA-only calculation. See the Tirion article in the References section.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 11:45 June 07, 2018.