Prediction Association Rate Enhancement

P A R E

Predicting Association Rate Enhancemet

This is an example for an INPUT data for the coarse rate calculation.

Calculating the rate of association between Ras(E31K ) and it's effector Ral at 4 different salt concentrations

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 k_on was determined experimentally:

file name:

Ras_Ral-human.pdb

Enter the experimental k_on of the above protein complex, and the ionic strength in which it was determined:

assocaition rate ionic strength

7.7e6 0.02

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 residues 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 , use the following format:
atom; res; res_num; chain; charge (press Return after each line)

O1G; GNP; 170; B; -0.6667

O2G; GNP; 170; B; -0.6667

O3G; GNP; 170; B; -0.6667

O1B; GNP; 170; B; -0.5

O2B; GNP; 170; B; -0.5

O1A; GNP; 170; B; -0.5

O2A; GNP; 170; B; -0.5

MG; MG; 373; *; 2.0

2) Calculating kon for the mutant protein.

enter the pdb file name of the protein file name

file name:

Ras_Ral-human.pdb

Enter the different salt concentration (M) in which you want to perform the calculation:

(press Return after each one)

	0.02
	0.05
	0.1
	0.25

Enter charge rules of your mutant for which you want kon to be calculated