Comparative Molecular Docking with Autodock Vina and Swissdock

Autodock Vina is an open source program that is used to perform docking molecule designed by Dr. Oleg Troot Molecular Graphics Lab at The Scripps Research Institute (http://vina.scripps.edu). Vina is a new generation software from Molecular docking Grapichs Lab, which has a binding mode prediction accuracy rate is high. The software can be operated with the help AutoDockTools (ADT) (http://autodock.scripps.edu/#VINA).

In this article I will discuss the results of molecular docking that I did use Autodock Vina and Swissdock. Protein Kinase I use is with pdb code 1IEP and ligand used imanitib with code STI-571. Here is the structure of the protein used.

Docking is done with a personal computer and have the following specifications:

• OS: Windows 7 Professional 32-bit
• System Model: HP G42 Notebook PC
• Processor: Intel (R) Core (TM) i3 CPU M 380 @ 2.53GHz, 2.5GHz ~
• Memory: 3072 MB RAM
• BIOS: Default System BIOS

The first thing to do will set the position in the docking protein by using AutoDockTools, such as changing some of the parameters that exist in the grid box (Size and center). The first experiments carried out using the same size and with a data center at an example. Affinity minimum energy of each experiment with Autodock Vina is as follows:

no	mode	seed	center			size			affinity (kcal/mol)	time
			x	y	z	x	y	z
1	9	-1245082496	11	90.5	57.5	22	24	28	-10.9	3′ 41”
2	8	1927972080							-12.9	4′ 11”
3	6	214428336	15	92	60.5	24	24	28	-12.7	3′ 23”
4	4	-1245082496							-13.0	3′ 20”
5	6	-1245082496	15	92	60.5	24	30	28	-12.9	4′ 05”
6	7						20		-12.1	4′ 01”
7	5					18	20	20	-9.9	3′ 29”
8	6					32	34	36	-13.0	3′ 48”
9	5					30	24	30	-13.0	4′ 38”
10	8					40	40	40	-9.7	4′ 27”
11	3					26	28	28	-13.2	3′ 15”
12	9					28	30	30	-10.8	3′ 41”
13	7	-1245082496	18	95	54	24	24	28	-12.7	3′ 49”
14	9	-2027272356							-10.9	3′ 19”

Experiments 1 and 2 was an experiment with size and center position equal to the sample, the minimum affinity resulting from the different experiments. Experiment 2 has a lower affinity than experiment 1, this is because the seeds are used differently. Experiment to 3 to 14 conducted by changing the size and center position, based on the trial minimum affinity obtained was -13.2 (ie experiment 11). Visualization of the structure of the ligand on trial 4, 5, 8, 9 and 11 is almost the same as the ligand experiment. Visualization of the results of docking on trial 11 using PyMOL are as follows

Experiment 5 to 12 use the same seed daerikut center, just change the size of the size. Based on these results the greatest affinity resulting from the experiment 10 with a value of -9.7 kcal / mol (size x: 40, y: 40, z: 40) and the smallest affinity resulting from the experiment 11 with a value of -13.2 kcal / mol. Based on the results of experiments conducted can be concluded that the minimum affinity obtained at a certain size, because the larger or the smaller the size, the size of the resulting greater affinity.

Experiments 13 and 14 using the center and the same size, but different seed so as to produce a different affinity. Minimum affinity of the two trials is -12.7 (experiment 11).

Besides Autodock Vina, the simulation can also be done with swissdock, which is a web service that is used to predict the possible interaction between target proteins and small molecules. The working principle is based on software Swissdock docking EADock DSS (http://www.swissdock.ch). The energy generated in the form swissdock free energy (ΔG). The minimum energy generated from experiments with swissdock using the same protein and ligand is -14.00 kcal / mol. Here are the results of visualization of swissdock by using PyMOL.