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Generating movies simulating the structural transition between two known forms of the same macromolecule

If you have two known forms of the same macromolecule, you can generate a movie that interpolates in a plausible way between these two forms.
A method allowing to do this without deforming too much the molecule and using the ideas of the Elastic Network has been published recently (see below).
The salient feature of this method is that it interpolates the interatomic distances, not the cartesian coordinates nor the dihedral angles. Therefore, the secondary structures tend to be preserved during the transition.

We have included some examples of such movies that were generated using a method which also uses the concept of Elastic Network Model (sometimes called morphing).
First, you need to superimpose the two structures (they should have the same number of CA atoms). You can do this using Profit.

Details on the morphing method can be found in the following publication:
Kim M.K., Jernigan R.L., Chirikjian G.S.
Efficient generation of feasible pathways for protein conformational transitions. Biophys J. (2002) 83:1620-30.

We have implemented this morphing method in Fortran and it can be run here (submit a job using the menu on the left):

Other methods are available elsewhere on the web, but based on different concepts:
-Mark Gerstein in Yale MolMovdb
-Gerard Kleywegt (esp. lsqman) in Uppsala USF

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 19:03 December 05, 2019.