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Saturday, August 11, 2012

PCA Plot

Continuing from the last post i have done some PCA anaylsis using 12 different physicochemical property descriptors including molecular refractivity, atom polarizabilities, bond polarizabilities, hydrogen bond donors and acceptors, petitjean number, topological polar surface area, number of rotatable bonds,liphophilicity XLogP, molecular weight, topological shape and geometrical shape. 

I used CDK for this developed by Rajarshi Guha and plotted the plot using ggplot2

Quite impressive that the compounds which have been screened was in the same area of the PknB inhibitors. Some outliers like Mitoxantrone,straurosporine are their which are scattered in plot . But majority of the predicted ones are in close association with the PknB inhibitors. 
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