Structure-selection

As described in the paper:

Theory and practice of using solvent paramagnetic relaxtion enhancement to characterize protein conformational dynamics

Zhou Gong, Charles D.Schwieters, ChunTang,  Methods, 148:48-56 (2018)

Contact: tanglab@wipm.ac.cn

 

What is Structure-selection

Structure-selection is a program that can identify the best combination of bio-molecule conformers from pre-generated conformation pool based on different type of experimental input. The program use a Monte Carlo (MC) simulated annealing method to identify an N-membered ensemble (N can be as few as 1), of which the averaged calculated values should be most consistent with experimental values. To assess the robustness of the method and the convergence of the ensemble structure, the MC simulated annealing is repeated 100 times, each from a randomly selected N-membered ensemble.

 

How to use Structure-selection

Run the program in a Linux system as the following command:

./mc-new.x (experiment file) (calculate file list) (number of MC steps) (number of conformers) (output file)

  • the experiment file should contain two column, one of the residue number and one of the experiment value
  • the calculate file list just need to specifiy the name of the calculated files, which should be pre-calculated before the selection. The calculated file should also contain two column same as the experiment file.
  • The number of MC steps should more than 10 times of the number of calculated files
  • The output file will give the name of selected file, ensemble averaged calculated values and correlation coefficient factor.

Example of output file

Resource files: 
AttachmentSize
Binary Data mc-new.x941.39 KB