Predicting Association Rate Enhancemet

*Read the instructions before using the program.

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)

Last modified: June 4,2001

For questions or suggestions please contact:
Gideon Schreiber