ProDy applications are command line programs that automates structure processing and structural dynamics analysis:
Running prody command will provide a description of applications:
$ prodyprody.txt
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 1p38In 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 1p38The output file p38_anm.nmd can be visualized using NMWiz.