Table 1: Summary of redocking results.

Complex PDB Res (Å) Receptorname Ligandname Docking results Crystal structures RMSDa (Å) Interaction energy (kcal mol−1) RMSD (Å) Interaction energy (kcal mol−1) Sequence number/total numberb Protease-inhibitor  1CA0 2.10 Chymotrypsin APPI 1.27 −93.70 0.84 −93.22 116522/492124  1CBW 2.60 Chymotrypsin BPTI 0.54 −83.51 0.19 −85.02 171485/456398  1ACB 2.00 Chymotrypsin Eglin C 1.00 −103.41 0.70 −103.49 382613/513612  1CHO 1.80 Chymotrypsin Ovonmuciod 0.30 −102.35 0.38 −102.42 302176/406978  1CGI 2.30 Chymotrypsinogen HPTI 0.18 −147.17 0.15 −147.10 34660/494274  2KAI 2.50 Kallikrein A BPTI 1.10 −114.68 0.21 −113.85 422991/576133  2SNI 2.10 Subtilisin BPN CI-2 0.27 −108.81 0.28 −108.86 232574/428140  2SIC 1.80 Subtilisin BPN SSI 0.89 −94.41 0.20 −104.20 109196/440000  1CSE 1.20 Subtilisin Carlsberg Eglin C 1.24 −98.28 0.088 −103.19 284340/470409  2TEC 1.98 Thermitase Eglin C 0.44 −108.55 0.68 −109.99 341844/565586  1TAW 1.80 Trypsin (bovine) APPI 1.10 −97.13 0.86 −97.14 374416/448887  2PTC 1.90 Trypsin (bovine) BPTI 0.98 −96.22 0.36 −96.25 269684/377757  3TGI 1.80 Trypsin (rat) BPTI 0.39 −102.43 0.52 −102.44 232589/511269  1BRC 2.50 Trypsin (rat) APPI 1.43 −90.55 0.55 −90.04 120053/527160 Enzyme-inhibitor  1FSS 3.00 Acetylcholinesterase Fasciculin II 0.17 −137.88 0.20 −137.88 356416/364018  1BVN 2.50 α-Amylase Tendamistat 0.25 −142.67 0.24 −142.51 202279/297696  1BGS 2.60 Barnase Barstar 0.48 −112.46 0.57 −112.37 326865/408756  1AY7 1.70 Ribonuclease sa Barstar 0.49 −77.41 0.51 −77.37 9999/356359  2B5R 1.70 TEM-1 lactamase BLIP 0.78 −154.04 0.37 −158.39 369/464219  1UGH 1.90 UDG UGI 0.54 −135.58 0.51 −135.43 120973/427026 Electron transport  2PCBc 2.80 Cyt c Peroxidase Cytochrome c 1.98 −87.18 0.22 −81.79 6060/416861  2PCF NMR Cytochrome f Plastocyanin 0.28 −118.96 0.23 −119.32 83197/208700 Antibody-antigen  1MLC 2.10 Fab D44.1 Lysozyme 1.59 −93.99 0.44 −95.80 75843/344243  1VFBd 1.80 Fv D1.3 Lysozyme 0.53 −84.78 0.43 −84.59 517225/1195007

aRMSDs are calculated for the atoms of the ligand protein since the receptor proteins are always fixed during the simulations. bSequence number denotes which sequence is the predicted conformation belonging to the BD sampling. Each conformation has unique sequence number as a label. Total number denotes how many compact complexes were obtained. From this column one can see where the final predicted complex(es) come from and how many compact complexes can be obtained from one million BD runs. These data are collected to demonstrate the necessary and sufficient condition for one million BD runs. cThe conformation presented here is the 9th conformation by energy ranking. The top 8 conformations are regarded as one cluster RMSD around 30 Å from the crystal structure (see Section 4). dThree million BD runs were conducted for this complex. Usually one million is enough for most complexes; however, due to the positive electrostatics 1.61 kcal mol−1 for this complex, the sampled near-native conformation appeared at around 1.4 million runs.