Generating the trajectory with minimum action between two conformational states of large macromolecular complexes

Reference: MinActionPath2.

This is an updated version of MinActionPath that generates the transition path between two known conformational states of the same macromolecular complex. It differs from existing morphing techniques by using the principle of least action (see also Ref.).
It can now handle very large data files and offers different ways to define the energy landscape (ENM or Go-like) and the neighbours (through a cutoff or by using Delaunay tessalation) in the pair-wise energy terms.

The program can process structures with a very large number of residues (e.g. 150,000) usually represented in a coarse-grained fashion with one atom (bead) per residue (usually the C-alpha for proteins).

It features an energy landscape based on the Elastic Network Model (ENM) or on the Go Model, described here.
Using the Go Model, there will be less deformations of the backbone of the proteins during the transition path, i.e. the geometry of the chain will be more preserved than with the ENM.

It also proposes a definition of neighbours using Delaunay tessalation as described here.
Using this method, the calculation will be more rapid (there are less neighbours per site) and unwanted "dangling effects" of loosely connected domains will be avoided.

References and validation:
MinActionPath old web server and More on the method.
Defining Neighbours using Delaunay
Normal Modes for Zika Virus
Go Energy Model for Zika Virus

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More on the Go-model:
It is designed in a such a way that the stereochemistry of proteins will be deformed minimally during the transition through the addition of several two-body energy terms : the bond length term, two elastic terms based on torsional and dihedral angles, and a non-local-term (vdw-like).

$V_{\mathrm{tot}}=V_{\mathrm{bond}}+V_{\mathrm{tor}}+V_{\mathrm{dihed}}+V_{\mathrm{non-local}}$

This form helps you to specify the two PDB input files and the parameters of the simulation.

Input:

You need two files (in PDB or CIF format) for the initial and final states of the transition you want to calculate.

Example (initial state)	:	8G34.cif
Example (final state)	:	8G31.cif

The two structures need not to have been structurally aligned beforehand, the program will do it anyway.
If the number of residues in the two files are different, the algorithm will attempt to match them and will work only with the common atoms. This is also true if there are different chains.
Energy can be as in the Elastic Network Model or as in the Go Model.
Neighbours in the two-body energy terms can be defined either with a cutoff (in Angstrom) or by Delaunay tessalation (no cutoff).
In the form itself, information on the fields that are to be filled in are contained in the blue "information" icon next to it.

Output:

The output files are the trajectory ("trajectory.cif.gz") and the coordinates of the transition state ("transition.cif"). Because the trajectory file can be very large (it contains 60 frames), it has been compressed (gzipped). To uncompress, simply type "gunzip file.gz" on a terminal.
In addition, the input files that have been pre-processed before being forwarded as input to MinActionPath2 are also downloadable as "initial_conformation_xxx.pdb" and "target_conformation_xxx.pdb" ("xxx" stands for any suffix; it reflects the modifiers that were applied).

Logfile:

In the logfile ("output.txt") you will find details on the progression of the algorithm, in particular in its search of the transition state.

1. Protein-DNA

   Initial conformation	:	2KTQ.pdb
   Target conformation	:	3KTQ.pdb
   MinActionPath2 results	:	2KTQ_to_3KTQ

2. DNA-Origami

   Initial conformation	:	7YWH.pdb
   Target conformation	:	7YWO.pdb
   MinActionPath2 results	:	7YWH_to_7YWO

3. Ribosome

   Initial conformation	:	8G34.cif
   Target conformation	:	8G31.cif
   MinActionPath2 results	:	8G34_to_8G31

4. Virus
   Depending on your internet bandwidth, this example might take a few minutes to load.
   You can watch the tutorial movie that showcases it instead.

   Initial conformation	:	Zika_pH5.pdb
   Target conformation	:	Zika_pH8.pdb
   MinActionPath2 results	:	Zika_pH5_to_pH8 (long to load)