Table 1 Δ Δ PT tools
From: Δ ΔPT: a comprehensive toolbox for the analysis of protein motion
Tool | Description |
|---|---|
G E N E N M M | Generates interaction matrix for an ENM |
D I A G S T D | Diagonalises an interaction matrix |
D I A G R T B | Diagonalises an interaction matrix with the RTB approximation |
D O M A I N S | Rewrites pdb into custom domain order for domain RTB |
G N M P R O D | Calculates the normal modes for a GNM |
F R E Q / E N | Calculates the frequencies and energies for a set of normal modes |
R M S / C O L | Calculates the motion, B-factors and collectivity for a set of normal modes |
C R O S C O R | Calculates the cross correlation for a set of normal modes |
O V E R L A P | Calculates the overlap of a set of normal modes |
G R O A M E D | Converts Gromacs and Amber output for use with the toolbox |
C O V A R | PCA decomposition for Gromacs, Amber, or DL_POLY trajectories |
F U L L 2 C A | Reduces outputs for full protein into C α only outputs |
T R A J P D B | Converts trajectories from Gromacs, Amber, or DL_POLY into a pbc fixed pdb file |
N M W I Z W T | Produces input for the nmwiz plugin for VMD |
P R O J E C T | Produces a set of pdb files for each normal mode perturbed from the input structure |
E G N P R O J | Plots the trajectory frames onto the eigenvector space |
P D B D I F F | Produces the vector between two pdb structures |
S P A C I N G | Calculates the inter-atom distances for plotting |
M O V E I N G | Calculates the change in atom positions due to the normal modes |
P L O T P D B | Writes a file of residue based values onto a pdb for plotting in VMD |