Table 1: Summary of redocking results.

Complex PDBRes (Å)ReceptornameLigandnameDocking resultsCrystal structures
RMSDa (Å)Interaction energy (kcal mol−1)RMSD (Å)Interaction energy (kcal mol−1)Sequence number/total numberb

Protease-inhibitor
 1CA02.10ChymotrypsinAPPI1.27−93.700.84−93.22116522/492124
 1CBW2.60ChymotrypsinBPTI0.54−83.510.19−85.02171485/456398
 1ACB2.00ChymotrypsinEglin C1.00−103.410.70−103.49382613/513612
 1CHO1.80ChymotrypsinOvonmuciod0.30−102.350.38−102.42302176/406978
 1CGI2.30ChymotrypsinogenHPTI0.18−147.170.15−147.1034660/494274
 2KAI2.50Kallikrein ABPTI1.10−114.680.21−113.85422991/576133
 2SNI2.10Subtilisin BPNCI-20.27−108.810.28−108.86232574/428140
 2SIC1.80Subtilisin BPNSSI0.89−94.410.20−104.20109196/440000
 1CSE1.20Subtilisin CarlsbergEglin C1.24−98.280.088−103.19284340/470409
 2TEC1.98ThermitaseEglin C0.44−108.550.68−109.99341844/565586
 1TAW1.80Trypsin (bovine)APPI1.10−97.130.86−97.14374416/448887
 2PTC1.90Trypsin (bovine)BPTI0.98−96.220.36−96.25269684/377757
 3TGI1.80Trypsin (rat)BPTI0.39−102.430.52−102.44232589/511269
 1BRC2.50Trypsin (rat)APPI1.43−90.550.55−90.04120053/527160

Enzyme-inhibitor
 1FSS3.00AcetylcholinesteraseFasciculin II0.17−137.880.20−137.88356416/364018
 1BVN2.50α-AmylaseTendamistat0.25−142.670.24−142.51202279/297696
 1BGS2.60BarnaseBarstar0.48−112.460.57−112.37326865/408756
 1AY71.70Ribonuclease saBarstar0.49−77.410.51−77.379999/356359
 2B5R1.70TEM-1 lactamaseBLIP0.78−154.040.37−158.39369/464219
 1UGH1.90UDGUGI0.54−135.580.51−135.43120973/427026

Electron transport
 2PCBc2.80Cyt c PeroxidaseCytochrome c1.98−87.180.22−81.796060/416861
 2PCFNMRCytochrome fPlastocyanin0.28−118.960.23−119.3283197/208700

Antibody-antigen
 1MLC2.10Fab D44.1Lysozyme1.59−93.990.44−95.8075843/344243
 1VFBd1.80Fv D1.3Lysozyme0.53−84.780.43−84.59517225/1195007

aRMSDs are calculated for the C 𝛼 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.