DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0

BMC Chemistry

Table 1 Docking results for eight Protein Data Bank (PDB) complexes using DOVIS 2.0.

PDB code	Receptor-ligand complex	All-atom model		Polar-hydrogen model
		RMSD (Å)	Score^a	RMSD (Å)	Score^a
186L	Lysozyme(L99A)/n-butylbenzene	0.59	3.33	0.80	4.03
1ABE	Arabinose-binding protein/α-L-arabinose	2.64	4.58	2.33	4.08
1BR6	Ricin A chain/pteroid acid	0.62	5.40	0.75	5.27
1KIM	Thymidine kinase/deoxythymidine	1.17	3.87	0.73	4.31
1RBP	Retinol-binding protein/retinol	1.98	-18.88	1.54	5.92
1STP	Streptavidin/biotin	0.83	5.16	0.81	5.31
3PTB	Trypsin/benzamidine	0.48	3.37	0.48	3.54
4DFR	Dihydrofolatereductase/methotrexate	5.06	4.59	5.03	4.23

Root mean square deviation (RMSD) values were calculated between the docked ligand poses and the X-ray ligand based on heavy atoms. The entries in the table show the lowest RMSD values and associated AutoDock 4.0 scores for docked ligand poses of eight PDB complexes. Typically, the difference in RMSD between the all-atom and the polar-hydrogen model is very small; the average absolute difference is 0.20 Å. ^a AutoDock 4.0 Score

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