Predicting Protein Interactions by Brownian Dynamics Simulations

Table 3

Comparison between docking with crystal packing and without crystal packing.

Complex PDB	Crystal packing		Without packing
	RMSD*(Å)	Interaction energy (kcal mol^−1)	RMSD*(Å)	Interaction energy (kcal mol^−1)
1CBW	0.72	−161.60	0.54	−83.51
1ACB	0.49	−131.61	1.00	−103.41
1CHO	0.23	−140.39	0.30	−102.35
1CGI	1.07	−138.82	0.18	−147.17
2KAI	0.98	−140.16	1.10	−114.68
2SNI	0.58	−120.52	0.27	−108.81
2SIC	1.44	−103.29	0.89	−94.41
2TEC	0.76	−127.74	0.44	−108.55
1TAW	0.44	−103.90	1.10	−97.13
1FSS	0.26	−175.90	0.17	−137.88

*RMSDs are calculated for the C_𝛼 atoms of the ligand protein.