Dear Professor Bryan Der,
Thank you very much for your great server. I've come across two essential questions using your techniques and I really need your help so I can continue working on my PhD thesis.
I've used both supercharge methods:
1- In terms of the Rosetta method , I assigned my "Target Net Charge Protein" to be negative. I was wondering if I need to disable (uncheck or untick) the rosetta positive supercharge options including ARG-LYS and enable (check or tick) the Rosetta negative supercharge options including ASP-GLU?
2- In order to use the AVNAPSA-Negative method, do I need to disable (untick) both the options of Rosetta positive supercharge( including ARG-LYS) and Rosetta negative supercharge (including ASP-GLU) ? What I mean is that do I have to untick the boxes for ASP-GLU-ARG-LYS?
Would you please assist me in this matter? Thank you so much in advance for your advise and assistance.It's highly appreciated.
Have you tried using it and had problems? Or are you asking for confirmation before you try using it? Just give it a try first. (Bryan isn't associated with Rosetta anymore, although I've sent this along for his input in case he happens to remember).
"To answer #1:
Including Arg/Lys/Asp/Glu determines what amino acids will be included in the search space. If the starting charge is +0, and the target charge is negative, excluding Arg/Lys would reduce the size of the search space. If the starting charge is -30 and the target charge is -10, Arg/Lys would be included/needed to make the net charge less negative.
If the starting charge is +0 and the target charge is negative, and Asp/Glu are unchecked, the target net charge cannot be reached. I forget if I included logic with exit conditions in these cases.
(As a minor point, the size of the search space is not really an important consideration since the backbone is fixed, the positions are restricted to the surface, and the residues are restricted to RKDE).
To answer #2:
The checkboxes for Asp/Glu/Arg/Lys will be ignored by the protocol if AvNAPSA mode is chosen. AvNAPSA always uses these mutations: For positive supercharging, mutate DENQ-->K. For negative supercharging, mutate RKQ-->E and N-->D."