Protein-Protein Docking Benchmark
From Christoph's Personal Wiki
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) | 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.[2] | |||||||
Source: Benchmark 1.0[4]
References
- ↑ 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.
- ↑ Chen R, Weng Z (2002). Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins, 47:281-294.
- ↑ Hubbard SJ, Thornton JM (1993). NACCESS. University College London: Department of Biochemistry and Molecular Biology.
- ↑ Chen R, Mintseris J, Janin J, Weng Z (2003). A protein-protein docking benchmark. Proteins: Structure, Function, and Genetics, 52:88-91.
