Protein-Protein Docking Benchmark 1.0
From Christoph's Personal Wiki
| 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.[1] | |||||||
Source: Benchmark 1.0[3]
See also
References
- ↑ 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.
