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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...
SplitPDF -SplitPDF.jar- is a ‘command-line driven’ Java-program, it splits a PDF-file by bookmarks into separated PDF’s. The bookmark is used as title for the newly created PDF. Extremely usefull and fast in a batch processing environment.