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Command line application to generate contact matrix from proteins (3D)
A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps).
Contact Maps can be used to understand...
ProteinArchitect facilitates the visual exploration of the architecture of proteins, including conserved domains, secondarystructure elements and structurally flexible regions, e.g. in the context of the analysis of protein superfamilies.