I would like to ask for advice on your recently published STRESS tool. I would like to use it to identify residues that might be involved in allostery, however in the case of surface critical residues, it currently reports only up to ten residues per binding pocket. Is there a way to "hack" the identify_high_confidence_BL_sites.py script (which writes this file) to write all such residues, according to some probability cutoff? (I’m a Perl programmer, with relatively limited python experience.) Thank you in advance.
In order to change the number of residues reported for each site, you may download and modify 2 of the C scripts (available on the stress github page)
For example, to modify the scripts such that the new limit is set to 15 residues (you can change this cutoff number to be any arbitrary value that you wish), do the following:
1) In the script bindingSiteMeasures.c, replace instances of "10" with "15" in lines 77, 79, 217, 219, 240, 242.
2) In the script surfaceProbe.c, I replace instances of "10" with "15" in lines 1227, 1229, 1235, 1237.
3) Recompile the source code and re-run the calculations.
However, with respect to the parameters in general, we should note that the parameters of the surface-site identification scheme were established using a known set of allosteric residues. That is, our parameters were established empirically to best capture known allosteric sites. The details of all this can be found in the Supplementary Materials of the paper, specifically in the Supp section 3.1-a-iii "Defining & Applying Thresholds to Select High-Confidence Surface-Critical Sites". Thus, we would advise against changing them, since again, they were empirically optimized.