Generate the MAP trajectory between two known conformations
This project has been selected and is being sponsored by Apple's ARTS program.
If you use the results of this web-site, please cite:
Franklin et al., Nucl. Ac. Res., 2007
as described in this Reference and the corresponding PDF.
This program calculates the most-probable trajectory between two known structural states of a protein,
in the sense of maximum-likelihood or Minimum Action invented by Onsager and Machlup (1953).
Hence the name MinActionPath, or MAP, trajectory.
It differs fundamentally from "morphing", which is purely numerical interpolation between 2 structures using either
internal angles or intramolecular distances, and which is breifly described in the menu item called Morphing.
Here the "real" trajectory is calculated using path-integral techniques (see References section).
The main approximation of the current implementation is that the energy landscape around each of the two states is harmonic; here we use the Elastic Network Model (ENM) centered on each state.
The crossing point between the two multi-dimensional potential curves is found iteratively by the program.
The program allows for two main situations (see Chart):
- a difference of energy between the 2 states (left panel)
- a different strength of the elastic constant for the 2 states (right panel)
Here are some more details about the theory behind this web site:
Joel's Notes p.1.
Joel's Notes p.2.
Joel's Notes p.3.
Joel's Notes p.4.
Joel's Notes p.5.
In the present version, the program works with CA-ONLY; it should not contain more than 1000 atoms (residues).
However, a new version has just been developed that allows for handling larger systems and will be put on-line shortly.
It directly generates a trajectory PDB file readable by PyMol,
The transition state coordinates are written in a separate file, as well as its energy and the final
minimized action Stot.
Here is the kind of Movie you can get using this method; this is a GIF movie for adenylate kinase
that can be seen by just clicking the icon; however, much better representations can be seen by downloading the Pymol-formatted
trajectory and viewing it with PyMol, VMD...
Use the following two commands to generate a C-alpha trace movie with PyMOL:
1) pymol trajectory_file.pdb
Pymol>set cartoon_trace, 1
2) Then change colors and play the movie...
3) You can also download the ligand (if any) separately and show it as CPK.
For VMD, just use the Trace or Tube representation in "Drawing Molecule" option.