Prediction Association Rate Enhancement

P A R E

Predicting Association Rate Enhancemet

Example 1:This is an example for an INPUT data for the accurate calculationrate of association of Ras(E31K) and it's effector Ral at 4 different salt concentrations.

The reference protein is the wild-type complex (Ras_Ral-human.pdb), and in the mutant complex Glu31 was mutated to Lys.

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 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; residue; residue number; 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 k_on for the mutant protein.

enter the coordinate file name:

file name:

Ras_E31Ka_Ral-human.pdb

Enter the different salt concentrations (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 complex: