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PAP : a protein analysis package
Author(s) -
Callahan T.,
Gleason W. B.,
Lybrand T. P.
Publication year - 1990
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s0021889890004228
Subject(s) - protein data bank (rcsb pdb) , ramachandran plot , protein data bank , graphics , computer science , plot (graphics) , computer graphics (images) , workstation , plotter , scatter plot , sequence (biology) , crystallography , protein structure , mathematics , operating system , biology , chemistry , biochemistry , statistics , machine learning , genetics
A program package has been assembled for the analysis of protein coordinates which are in the Brookhaven Protein Data Bank (PDB) format. These programs can be used to make two types of ϕ – ψ plots: a Ramachandran‐style scatter plot, and a plot of ϕ and ψ values as a function of the linear sequence. Programs are also available for the display of distance diagonal plots for proteins. Two protein structures can be compared and the resulting r.m.s. differences in the structures plotted as a function of sequence. Temperature factors can be analyzed and plotted as a function of the linear sequence. In addition, various utilities are supplied for splitting PDB files which contain multiple subunits into individual files and also for renumbering PDB files. A utility is also provided for converting Amber‐style PDB files into standard PDB files. Priestle's program RIBBON [ J. Appl. Cryst . (1988), 21 , 572–576] has been converted to run in a stand‐alone mode with interactive rotation of the three‐dimensional ribbon picture. Programs are Silicon Graphics four‐dimensional level and have been tested on 4D70/GT and personal Iris workstations, although programs which give Postscript output have been converted to run on Digital Equipment Corporation VAX computers and Sun workstations.