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Find elastic constant by fitting calculated and exptal B-factors

Method
The ENM allows to calculate &Delta r2 for each atom, once the normal mode eigenvalues and eigenvectors are known. By comparing the predicted values to the ones inferred from the measured B-factors (B=8/3 &pi2 &Delta r2), one can deduce the value of the elastic constant that best reproduces the experimental values.

Your email adress: (Recommended, for notification)


Job title: (Only alphanumerical characters)


PDB file name (Max. 2000 residus)
(CA only for proteins, 3 atoms per nucleotide for nucleic acids)
Ex: 1OMP_ca.pdb


Number of modes (Max. 500)


Cutoff radius (Angstroms)



Output
The elastic constant (C) is the inverse of the Scale-factor (S) on output of the program.
On average, you expect S ~ 9.4 +/-5.5 for the scale factor (Yves-Henri Sanejouand, personal communication). This is true only for CA-only models (for all-atoms models, we expect different statistics). This implies the following range for the elastic constant:
C ~ 0.07-0.25 kcal/Mol/A2.

This assumes a Temperature of 300K. If the experiment was conducted in 100K, the elastic constant should be multiplied by 300/100, if one wants to compare to a structure that was solved at 300K.

This is intended to be used prior to the "Trajectory" Option on both the start AND end conformations of the molecule.

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 files should be in PDB format, with only a single structure (no multiple models). The limit is 2000 residues. For proteins, only CA atoms are accepted at this stage. For nucleic acids we recommend 3 atoms (P, C1' and C4') per nucleotide.

  • If you have more than 6 modes with zero frequency, this means that you have more than one rigid-body inyour model. Most probably there is an error in the generation of the biologically relevant multimer. You may also increase the cutoff radius of the ENM.

  • This is based on Y.H. Sanejouand's code...



  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 19:21 July 06, 2009.