1) Entering experimental data for the reference protein.
Enter the file name containing the protein complex coordinates (wt or mutant) for which the association rate (kon) was determined experimentally:
file name:
Enter the experimental kon of the above protein complex, and the ionic strength (M) in which it was determined:
association rate:
ionic strength:
Constructing the charge-file:
The following charge rules are incorporated in the program's charge file (charge is also assigned by the program to the N-termini of both proteins in the complex).
atom |
res |
num |
chain |
charge |
NZ |
LYS |
* |
* |
1.0 |
NH1 |
ARG |
* |
* |
0.5 |
NH2 |
ARG |
* |
* |
0.5 |
OE1 |
GLU |
* |
* |
-0.5 |
OE2 |
GLU |
* |
* |
-0.5 |
OD1 |
ASP |
* |
* |
-0.5 |
OD2 |
ASP |
* |
* |
-0.5 |
OXT |
* |
* |
* |
-1.0 |
|
In cases where modifications were made in one of the proteins, so that charges should be added or deleted (see help
), use the following format: atom; residue; residue number; chain; charge (press Return after each line)
|
2) Calculating kon for the mutant protein.
enter the file name containing the coordinates of the mutant complex:
file name:
Enter the different salt concentration (M) in which you want to
perform the calculation:
(press Return after each one)
Enter the charge rules of your mutant:
(press Return after each line)
|