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Table 3 Final Results of HopDock presented in this work.

From: HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking

PDB ID (Chains) Size Budda [9] (Å) Prev. [16] (Å) pyDock [4] (Å) ClusPro [6] (Å) HopDock (Å)
1C1Y (A,B) 2034 1.2 1.3 10.4 7.2 1.9
1DS6 (A,B) 2839 1.2 1.8 0.8 1.7 3.4
1TX4 (A,B) 2957 1.4 2.4 18.5 4.7 1.0
1WWW (W,Y) 1644 11.4 2.2 18.2 17.2 2.2
1FLT (V,Y) 1528 1.5 1.1 2.8 4.7 1.5
1IKN (A,C) 3178 1.2 2.0 20.1 19.7 2.2
1IKN (C,D) 2505 2.0 2.0 16.7 20.9 4.6
1VCB (A,B) 1447 0.7 2.1 1.4 1.9 3.6
1VCB (B,C) 1846 1.3 1.3 22.7 1.9 1.7
1OHZ (A,B) 1443 1.8 1.7 7.5 3.3 2.2
1T6G (A,C) 4022 1.6 2.5 0.1 14.8 2.5
1ZHI (A,B) 2633 25.3 1.7 23.8 24.1 3.3
2HQS (A,C) 3983 29.1 2.2 15.2 16.6 2.6
1QAV (A,B) 1503 1.4 1.0 9.6 1.7 2.6
1G4Y (B,R) 1838 0.8 2.3 26.2 1.9 4.1
1CSE (E,I) 2442 0.7 1.5 13.2 1.1 2.7
1G4U (R,S) 4188 1.0 2.2 27.6 16.1 5.6
  1. A comparative analysis has been performed on all seventeen dimers. For the comparison, two geometry-based (Budda [9] and work in [16]) and two energy-based methods (pyDock [4] and ClusPro [6]) have been chosen. Lowest lRMSD to native structure is reported for Budda in column 3, work in [16] in column 4, pyDock in column 5, ClusPro in column 6, and HopDock in column 7.