Predicting Protein Interactions by Brownian Dynamics Simulations

Table 2

Redocking results compared with other groups.

Complex PDB	RMSD (Å)^a	Other docking methods
		ICM^b	Nussinov^c	FTDOCK^d	BiGER^e
Protease-inhibitor
1CA0	0.44	0.4	—	—	—
1CBW	0.24	0.5	—	—
1ACB	0.58	0.5	0.9	—	0.6
1CHO	0.26	0.3	0.5	0.8	—
1CGI	0.15	0.4	—	1.0	—
2KAI	0.30	0.8	1.2	0.4
2SNI	0.16	0.3	1.1	0.6	—
2SIC	0.58	0.4	1.1	0.8	3.8
1CSE	0.53	0.3	1.3	—	—
2TEC	0.18	0.3	1.2	—	3.6
1TAW	0.39	0.7	—	—	—
2PTC	0.72	0.4	0.6	0.7
3TGI	0.21	0.3	—	—	—
1BRC	0.55	0.7	—	—	—
Enzyme-inhibitor
1FSS	0.13	0.4	—	—	—
1BVN	0.23	0.4	—	—	—
1BGS	0.33	0.6	—	—
1AY7	0.30	0.7	—	—
2B5R	0.60	1.3	—	—	—
1UGH	0.39	0.4	—	—	—
Electron transport
2PCB	1.18	1.2	—	—	—
2PCF	0.19	1.1	—	—	—
Antibody-antigen
1MLC	0.57	0.4	—	0.8	—
1VFB	0.24	0.5	1.5	0.7	—

^aRMSDs are calculated for the ligand interface C_𝛼 atoms in this work. ^bDocking with known binding site followed by refinement of interface side-chain conformations [27]; RMSD (Å) calculated for the ligand interface C_𝛼 atoms. ^cGlobal docking followed by hydrophobicity and connectivity filters [40]; RMSD (Å) calculated for the ligand heavy atoms when only receptor is superimposed onto the real structure. ^dGlobal docking and filtering with distance restraints [6]; RMSD (Å) when both receptor and ligand C_𝛼 atoms are superimposed onto the real complex. ^eGlobal docking [41]; RMSD (Å) calculated for the ligand C_𝛼 atoms when only the receptor C_𝛼 atoms are superimposed onto the real structure.