Protein-Protein Docking Benchmark

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A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods[1]. The set is chosen to cover a wide range of interaction types, and to avoid repeated features, such as the profile of interactors' structural families according to the SCOP database. Benchmark elements are classified into three levels of difficulty (the most difficult containing the largest change in backbone conformation). The protein-protein docking benchmark contains examples of enzyme-inhibitor, antigen-antibody and homomultimeric complexes.

Benchmark table

Benchmarks
Complexa Receptora Liganda Receptor description Ligand description RMSDb(Å) c ΔASAd2)
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.[2]
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.[3]

Source: Benchmark 1.0[4]

References

  1. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z (2005). Protein-Protein Docking Benchmark 2.0: an Update. Proteins, 60(2):214-6.
  2. Chen R, Weng Z (2002). Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins, 47:281-294.
  3. Hubbard SJ, Thornton JM (1993). NACCESS. University College London: Department of Biochemistry and Molecular Biology.
  4. Chen R, Mintseris J, Janin J, Weng Z (2003). A protein-protein docking benchmark. Proteins: Structure, Function, and Genetics, 52:88-91.