[rDock-list-def] Some general questions from a newbie

[Callan R. <sup...@ho...>]

Hi all,

Please forgive my basic questions - unfortunately I could not find clear answers from looking in the manual.

First off, when I am comparing docking poses, should I be focussing on <SCORE> or <SCORE.INTER>? The manual states "S Inter is the main term of interest as it represents the protein-ligand (or RNA-ligand) interaction score", but when I brought this up with my project supervisor he assured me to just use total score. I am still unsure of this based on some of the results I have generated.

Secondly, are these score values representative of free binding energy, as with some other programs? If so, are they given in kJ/mol or kCal/mol? Searching the manual for these units did not seem to yield any clear statement of one or the other, but both appeared in the document so I can't make any assumptions.

Thanks so much for your time!
Cal