Description: PMTmodel takes a modified pdb file and returns a dynamic probability file formatted into one column
Select properly formatted files:
PDBid.coo file:

Initial Probability file (Optional):

 Formatting instructions: The input file must be prepared in the following format:
  • File name must be pdbid.coo
  • First row contains only one integer, which equals to total number of residues in the structure
  • Second row contains only one integer, which equals to total number of atoms in the structure
  • Third row and beyond, for each atom in the structure create four columns:
    • Column one is the residue index
    • Column two is x coordinate
    • Column three is y coordinate
    • Column four is z coordinate
    example file:1p22.coo
Optional: In addition, feel free to upload your own initial probability file. If omitted, PMTmodel will default to uniform probability. The input file must be prepared in the following format:
  • Filename must be pdbid.ini
  • It only has one column; number of rows, which equal to total number of residues in the structure
  • Each row contains only one value, which equals to the initial probability of each residue (sum up equal to 1)
    example file:1p22.ini
Download Compiled Binary File for Linux
 We have provided PMT model in a downloadable form so it can be run on your personal machine. This package includes binary executable files, which were compiled on:
  • Intel CPU
  • Linux kernel 2.6.18 i386 (32 bits)
  • CentOS release 5.4
  • g++ (GCC) 4.1.2
  • GNU Fortran (GCC) 3.4.6
    Instruction and example files are also included.
    Downlaod: pmt_linux.tar
Please cite the following if you publish or present results using the PMT model:
Hsiao-Mei Lu and Jie Liang (2009), Perturbation-based Markovian Transmission Model for Probing Allosteric Dynamics of Large Macromolecular Assembling: A Study of GroEL-GroES, PLoS Comput. Biol. 5(10):e1000526. pdf file 1.2M