We are intensively working on extensions focused on RMSD calculation, scripting possibilities, or advanced work with biomolecules containing standard residues.
Molecular volumes calculations of FPP and FPP analogues were performed using the volume calculation script from Schrodinger, version 9.3.
AG and JC designed the main algorithm and developed the PERL STRING processing scripts and R Similarity calculations scripts.
For calculation the script ANI.pl (by Jiapeng Chen) available at https://github.com/chjp/ANI was used taking one strain of a pair as query and the other one as reference and vice versa.
This paper focuses exclusively on precisely describing the conception of the algorithms, architecture and how geo-processing is done rather than providing line per line calculation details and scripts.
Sliding windows analysis, statistical calculation, and permutation scripts were written with the R package [74].
The ensemble is established nicely in the premiere, despite the obvious calculation in the script and casting.
In order to begin calculation, the Matlab script was initialized with the coordinates of GasFinder unit and retroreflector positions (Figs. 2 and 3).
The scripts for calculation of ICs (polar/apolar/charged divided) and NIS are available at: http://bonvinlab.org/software.
For calculation of difference maps scripts from the CCP4 program suite package were manually modified and used at each step as indicated in brackets.
We implemented this calculation in a Perl script available upon request by the authors.
