visualizeprot: visualizeprot: Get a quick chemical representation of the...
In zalperst/visualizeprot: Visualize the Protein Chemical Property Landscape

Although the gold standard for understanding is usually thought to be through imagery in the spatial domain, such an endeavour becomes impossible as complexity increases. Therefore it may be a useful alternative to reduce the 3 spatial dimensions into a linear coordinate and plot a chemical property on the y-axis. I have chosen to plot logP values across an atom coordinate. LogP is a measurement of the affinity of a compound for octanol over water (more negative means more hydrophilic). I have chosen to process a pdb object rendered by the package "Rpdb" into a tibble, assign logPs and a acidity class (acidic, basic or neutral) based on the amino acid sequence. The logP values have been calculated and can be found at http://www2d.biglobe.ne.jp/~chem_env/amino/amino2j_e.html and are also commented in the function assign_params(). The typical work flow is as follows, first one reads in a pdb file with Rpdb, followed by processing with the pdb_dataframe() function from this package. After this one assigns logP and acidity categories with assign_params() and finally one chooses their plot of interest which is either categorical (acidity_landscape(), discriminate based on color), or numeric (with polar_landscape()). Alternatively, one can plot each on the same plot with full_landscape to match up the two. Interesting questions one might try to answer with this package are: "can I identify functional regions based on patterns of high polarity amino acids/ functional amino acids", " what are the structural/ functional differences between regions that are polar but not acidic? could this represent a protein:protein interaction region?"

zalperst/visualizeprot documentation built on May 4, 2019, 9:08 p.m.