ProDy Applications

ProDy applications are command line programs that automates structure processing and structural dynamics analysis:

• prody align
• prody anm
• prody biomol
• prody blast
• prody catdcd
• prody contacts
• prody eda
• prody fetch
• prody gnm
• prody pca
• prody select

Running prody command will provide a description of applications:

$ prody

usage: prody [-h] [-c] [-v]
             {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select}
             ...

ProDy: A Python Package for Protein Dynamics Analysis

optional arguments:
  -h, --help            show this help message and exit
  -c, --cite            print citation info and exit
  -v, --version         print ProDy version and exit

subcommands:
  {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select}
    anm                 perform anisotropic network model calculations
    gnm                 perform Gaussian network model calculations
    pca                 perform principal component analysis calculations
    eda                 perform essential dynamics analysis calculations
    align               align models or structures
    blast               blast search Protein Data Bank
    biomol              build biomolecules
    catdcd              concatenate dcd files
    contacts            identify contacts between a target and ligand(s)
    fetch               fetch a PDB file
    select              select atoms and write a PDB file

See 'prody <command> -h' for more information on a specific command.

Detailed information on a specific application can be obtained by typing the command and application names as prody anm -h.

Running prody anm application as follows will perform ANM calculations for the p38 MAP kinase structure, and will write eigenvalues/vectors in plain text and NMD Format:

$ prody anm 1p38

In the above example, the default parameters (cutoff=15. and gamma=1.) and all of the Cα atoms of the protein structure 1p38 are used.

In the example below, the cutoff distance is changed to 14 Å, and the Cα atoms of residues with numbers smaller than 340 are used, the output files are prefixed with p38_anm:

$ prody anm -c 14 -s "calpha resnum < 340" -p p38_anm 1p38

The output file p38_anm.nmd can be visualized using NMWiz.