Protein-Protein Docking Benchmark 1.0

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Protein-Protein Docking Benchmark 1.0
Complexa Receptora Liganda Receptor description Ligand description RMSDb(Å) Cαc ΔASAd(Å2)
Enzyme-inhibitor (22)
Unbound-unbound (16)
1ACB(E:I) 5CHA(A) 1CSE(I) α-Chymotrypsin Eglin C 0.7 1 1540
1AVW(A:B) 2PTN 1BA7(A) Trypsin Soybean trypsin inhibitor 0.35 0 1740
1BRC(E:I) 1BRA 1AAP(A) Trypsin APPI 0.44 0 1320
1BRS(A:D) 1A2P(B) 1A19(A) Barnase Barstar 0.47 0 1560
1CGI(E:I) 1CHG 1HPT α-Chymotrypsinogen Pancreatic secretory trypsin inhibitor 1.48 14 2050
1CHO(E:I) 5CHA(A) 2OVO α-Chymotrypsin Ovomucoid 3rd domain 0.59 1 1470
1CSE(E:I) 1SCD 1ACB(I) Subtilisin Carlsberg Eglin C 0.43 0 1490
1DFJ(I:E) 2BNH 7RSA Ribonuclease inhibitor Ribonuclease A 1.04 13 2580
IFSS(A:B) 2ACE(E) 1FSC Snake venom acetylcholinesterase Fasciculin II 0.75 1 1970
1MAH(A:F) 1MAA(B) 1FSC Mouse acetylcholinesterase Fasciculin II 0.6 0 2150
1TGS(Z:I) 2PTN 1HPT Trypsinogen Pancreatic secretory trypsin inhibitor 1.49 17 1720
1UGH(E:I) 1AKZ 1UGI(A) Human Uracil-DNA glycosylase Inhibitor 0.53 1 2190
2KAI(AB:I) 2PKA(XY) 6PTI Kallikrein A Trypsin inhibitor 0.7 2 1420
2PTC(E:I) 2PTN 6PTI β-Trypsin Pancreatic trypsin inhibitor 0.32 0 1430
2SIC(E:I) 1SUP 3SSI Subtilisin BPN Subtilisin inhibitor 0.4 0 1620
2SNI(E:I) 1SUP 2C12(I) Subtilisin Novo Chymotrypsin inhibitor 2 0.37 0 1630
Unbound-bound (6)
1PPE(E:I) 2PTN 1PPE(I) Trypsin CMT-I 0.27 0 1690
1STF(E:I) 1PPN 1STF(I) Papain Stefin B 0.25 0 1790
1TAB(E:I) 2PTN 1TAB(I) Trypsin BBI 0.27 0 1360
1UDI(E:I) 1UDH 1UDI(I) Virus Uracil-DNA glycosylase Inhibitor 0.36 0 2020
2TEC(E:I) 1THM 2TEC(I) Thermitase Eglin C 0.19 0 1560
4HTC(LH:I) 2HNT(LCEF) 4HTC(I) A-Thrombin Hirudin 0.56 2 3320
Antibody-antigen (19)
Unbound-unbound (5)
1AHW(DE:F) 1FGN(LH) 1BOY Antibody Fab 5G9 Tissue factor 0.71 1 1900
1BVK(DE:F) 1BVL(LH) 3LZT Antibody Hulysll Fv Lysozyme 1.22 3 1400
1DQJ(AB:C) 1DQQ(LH) 3LZT Hyhel-63 Fab Lysozyme 0.73 3 1760
1MLC(AB:E) 1MLB(AB) 1LZA IgG1 D44.1 Fab fragment Lysozyme 0.85 3 1390
1WEJ(LH:F) 1QBL(LH) 1HRC IgG1 E8 Fab fragment Cytochrome C 0.32 0 1180
1BQL(LH:Y) 1BQL(LH) 1DKJ Hyhel-5 Fab Lysozyme 0.52 2 1630
1EO8(LH:A) 1EO8(LH) 2VIU(A) Bh151 Fab Influenza virus hemagglutinin 0.28 0 1530
1FBI(LH:X) 1FBI(LH) 1HHL IgG1 Fab fragment Lysozyme 0.5 0 1690
1IAI(MI:LH) 1AIF(LH) 1IAI(LH) IgG1 Idiotypic Fab Igg2A anti-idiotypic Fab 0.99 12 1890
1JHL(LH:A) 1JHL(LH) 1GHL(A) IgG1 Fv fragment Lysozyme 0.26 0 1240
1KXQ(D:E) 1PIF(A) 1KXQ(E) α-Amylase Camelid AMD9 Vhh domain 0.43 0 2140
1KXT(A:B) 1PIF(A) 1KXT(B) α-Amylase Camelid AMB7 Vhh domain 0.39 0 1620
1KXV(A:C) 1PIF(A) 1KXV(C) α-Amylase Camelid AMD10 Vhh domain 0.24 0 1620
1MEL(B:M) 1MEL(B) 1LZA Vh single-domain antibody Lysozyme 0.65 2 1690
1NCA(LH:N) 1NCA(LH) 7NN9 Fab NC41 Influenza virus neuraminidase 0.24 0 1950
1NMB(LH:N) 1NMB(LH) 7NN9 Fab NC10 Influenza virus neuraminidase 0.21 0 1350
1QFU(LH:A) 1QFU(LH) 2VIU(A) Igg1-k Fab Influenza virus hemagglutinin 0.27 0 1840
2JEL(LH:P) 2JEL(LH) 1POH Jel42 Fab fragment A06 phosphotransferase 0.18 0 1500
2VIR(AB:C) 2VIR(AB) 2VIU(A) Igg1-lamda Fab Influenza virus hemagglutinin 0.41 1 1260
Others (11)
Unbound-unbound (5)
1AVZ(B:C) 1AVV 1SHF(A) HIV-1 NEF FYN tyrosin kinase SH3 domain 0.73 1 1260
1L0Y(A:B) 1BEC 1B1Z(A) T-cell receptor β chain Exotoxin A1 0.83 2 1130
1WQ1(G:R) 1WER 5P21 RAS activating domain RAS 0.83 9 2910
2MTA(LH:A) 2BBK(LH) 1AAN Methylamine dehydrogenase Amicyanin 0.34 0 1460
2PCC(A:B) 1CCA 1YCC Cytochrome C peroxidase Iso-1-Cytochrome C 0.44 1 1140
Unbound-bound (6)
1A0O(A:B) 1CHN 1A0O(B) Che A Che Y 1.59 9 1130
1ATN(A:D) 1ATN(A) 3DNI Actin Deoxyribonuclease I 0.31 0 1770
1GLA(G:F) 1GLA(G) 1F3G Glycerol kinase GSF III 0.37 0 1300
1IGC(LH:A) 1IGC(LH) 1IGD IgG1 Fab fragment Protein G 0.74 1 1330
1SPB(S:P) 1SUP 1SPB(P) Subtilisin Subtilisin prosegment 0.35 0 2230
2BTF(A:P) 2BTF(A) 1PNE β-Actin Profilin 0.29 0 2060
Difficult test cases (7)
Unbound-unbound (5)
1BTH(LH:P) 2HNT(LCEF) 6PTI Thrombin mutant Pancreatic trypsin inhibitor 1.91 18 2370
1FIN(A:B) 1HCL 1VIN CDK2 cyclindependant kinase 2 Cyclin 4.66 59 3400
1FQ1(B:A) 1B39(A) 1FPZ(F) CDK2 KAP 3.55 23 1830
1GOT(A:BG) 1TAG 1TBG(AE) Transducin Gt-α, Gi-α chimera Gt-β-γ 2.45 30 2500
1KKL(AC:H) 1JB1 1SPH(A) HPr kinase Phosphocarrier protein Hpr 2.53 28 1640
Unbound-bound (2)
1EFU(A:B) 1D8T(A) 1EFU(B) E. coli Ef-Tu Efts 2.57 109 3630
3HHR(B:A) 3HHR(B) 1HGU Human growth hormone Receptor 2.04 24 4150
a Four-letter PDB code for the crystal structures used in this study with chain IDs in parenthesis.

b The RMSD of the interface Cα atoms for input receptor and ligand after superposition onto the co-crystallized complex structure, calculated as in our previous work.[1]
c Number of interface Cα atoms with RMSD larger than 2Å between unbound and bound structures after superposition.
d ΔASA: change in accessible surface area (ASA) on complex formation was calculated, by using the program NACCESS.[2]

Source: Benchmark 1.0[3]


See also

References

  1. ↑ Chen R, Weng Z (2002). Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins, 47:281-294.
  2. ↑ Hubbard SJ, Thornton JM (1993). NACCESS. University College London: Department of Biochemistry and Molecular Biology.
  3. ↑ Chen R, Mintseris J, Janin J, Weng Z (2003). A protein-protein docking benchmark. Proteins: Structure, Function, and Genetics, 52:88-91.
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