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Coarse-graining by Decimation of a PDB file

The aim is to build a new Elastic Network Model from the initial classical Tirion model that still captures all the eseential features of the dynamics but iteratively eliminates atoms in such a way as to discard high-frequency modes.
In the Tirion model atoms are linked if their distance is less than a given threshold (radius).
To update this Network the following procedure is adpoted: individual frequencies are assigned to each atom, and, at each cycle, the atom with maximum frequency is eliminated. The links between its neighbours are re-defined and a new cycle begins until there remains a user-specified fraction of the initial number of atoms.

The method is derived from a renormalisation procedure initially derived in the statisticals physics of disordered materials and described by T. Garel and C. Monthus (PDF).
See here for an (Illustration).

You need a single input pdb file and the program will calculate the new links between the remaining atoms of the initial Elastic Network Model.
We recommand to proceed in two steps: first go though the Coarse-Graining procedure based on Names, or on the projection of the Hessian, before going to this step.

There will be one output PDB file per mode, named output.pdb, and an elastic.pml file representing the strength of the spring constants between remaining atoms by a color code, directly loadable by PyMol or VMD.

Because the strengths between the nodes have been modified, it becomes possible to look for preferred paths between 2 binding sites of the molecules, namely allosteric paths.

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters, no space)

PDB file for which you want to perform decimation
(Protein Ex: GLIC_open_ca.pdb). N.B. No Hydrogen atoms!

Radius for the initial Elastic Network Model (A)
Initial elastic constant between atoms (kT/A^2)

Selecting atoms in the PDB (proteins or nucleic acids)? (* for all atoms, CA for C-alpha only...)

Fraction of initial number of atoms to be left after decimation

Comment on Fraction It is useful to look at the log-file to adjust the fraction: usually there is point in decimation where all points start to be connected to all the others: this is where things begin to be interesting. The minimal number of connections is reported at every cycle of decimation (this is the last number on the line).

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 (ATOM card) are in the file will be used for the calculation (CAREFUL: but not the HETATM ones!). It is not recommanded to include Hydrogen atoms in the PDB file.

  • As a bonus, you will files to help visualize the new Elastic Net associated to your (decimated) protein leading to pictures like this: GLIC.png from a file downloadable by Pymol GLIC.pml.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 15:39 May 08, 2017.