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.
See also Supplementary Information
Protein-Protein Docking Benchmark 2.0
| Protein-Protein Docking Benchmark 2.0 | |||||||
|---|---|---|---|---|---|---|---|
| Complex | Cat.a | PDBid 1 | Protein 1 | PDBid 2 | Protein 2 | RMSDb (Å) | DASAc (Å2) |
| Rigid-body (63) | |||||||
| 1AVX(A:B) | E | 1QQU(A) | Porcine trypsin | 1BA7(B) | Soybean trypsin inhibitor | 0.47 | 1585 |
| 1AY7(A:B) | E | 1RGH(B) | Barnase | 1A19(B) | Barstar | 0.54 | 1237 |
| 1BVN(P:T) | E | 1PIG | α-amylase | 1HOE | Tendamistat | 0.87 | 2222 |
| 1CGI(E:I) | E | 2CGA(B) | Bovine chymotrypsinogen | 1HPT | PSTI | 2.02 | 2053 |
| 1D6R(A:I) | E | 2TGT | Bovine trypsin | 1K9B(A) | Bowman–Birk inhibitor | 1.14 | 1408 |
| 1DFJ(E:I) | E | 9RSA(B) | Ribonuclease A | 2BNH | Rnase inhibitor | 1.02 | 2582 |
| 1E6E(A:B) | E | 1E1N(A) | Adrenoxin reductase | 1CJE(D) | Adrenoxin | 1.33 | 2315 |
| 1EAW(A:B) | E | 1EAX(A) | Matriptase | 9PTI | BPTI | 0.54 | 1866 |
| 1EWY(A:C) | E | 1GJR(A) | Ferredoxin reductase | 1CZP(A) | Ferredoxin | 0.80 | 1502 |
| 1EZU(C:AB) | E | 1TRM(A) | D102N trypsin | 1ECZ(AB) | Ecotin | 1.21 | 2751 |
| 1F34(A:B) | E | 4PEP | Porcine pepsin | 1F32(A) | Ascaris inhibitor 3 | 0.93 | 3038 |
| 1HIA(AB:I) | E | 2PKA(XY) | Kallikrein | 1BXB | Hirustatin | 1.40 | 1737 |
| 1MAH(A:F) | E | 1J06(B) | Acetylcholinesterase | 1FSC | Fasciculin | 0.61 | 2145 |
| 1PPE(E:I) | E | 1BTP | Bovine trypsin | 1LU0(A) | CMTI-1 squash inhibitor | 0.44 | 1688 |
| 1TMQ(A:B) | E | 1JAE | α-amylase | 1B1U(A) | RAGI inhibitor | 0.86 | 2401 |
| 1UDI(E:I) | E | 1UDH | Uracyl-DNA glycosylase | 2UGI(B) | Glycosylase inhibitor | 0.90 | 2022 |
| 2MTA(HL:A) | E | 2BBK(JM) | Methylamine dehydrogenase | 2RAC(A) | Amicyanin | 0.41 | 1461 |
| 2PCC(A:B) | E | 1CCP | Cyt C peroxidase | 1YCC | Cytochrome C | 0.39 | 1141 |
| 2SIC(E:I) | E | 1SUP | Subtilisin | 3SSI | Streptomyces subtilisin inhibitor | 0.36 | 1617 |
| 2SNI(E:I) | E | 1UBN(A) | Subtilisin | 2CI2(I) | Chymotrypsin inhibitor 2 | 0.35 | 1628 |
| 7CEI(A:B) | E | 1UNK(D) | Colicin E7 nuclease | 1M08(B) | Im7 immunity protein | 0.70 | 1384 |
| 1AHW(AB:C) | A | 1FGN(LH) | Fab 5g9 | 1TFH(A) | Tissue factor | 0.69 | 1899 |
| 1BVK(DE:F) | A | 1BVL(BA) | Fv Hulys11 | 3LZT | HEW lysozyme | 1.24 | 1321 |
| 1DQJ(AB:C) | A | 1DQQ(CD) | FAB Hyhel63 | 3LZT | HEW lysozyme | 0.75 | 1765 |
| 1E6J(HL:P) | A | 1E6O(HL) | FAB | 1A43 | HIV-1 capsid protein p24 | 1.05 | 1245 |
| 1JPS(HL:T) | A | 1JPT(HL) | FAB D3H44 | 1TFH(B) | Tissue factor | 0.51 | 1852 |
| 1MLC(AB:E) | A | 1MLB(AB) | FAB44.1 | 3LZT | HEW lysozyme | 0.60 | 1392 |
| 1VFB(AB:C) | A | 1VFA(AB) | Fv D1.3 | 8LYZ | HEW lysozyme | 1.02 | 1383 |
| 1WEJ(HL:F) | A | 1QBL(HL) | FAB E8 | 1HRC | Cytochrome C | 0.31 | 1177 |
| 2VIS(AB:C) | A | 1GIG(LH) | FAB | 2VIU(ACE) | Flu virus hemagglutinin | 0.80 | 1296 |
| 1A2K(C:AB) | O | 1QG4(A) | Ran GTPase | 1OUN(AB) | Nuclear transport factor 2 | 1.11 | 1603 |
| 1AK4(A:D) | O | 2CPL | Cyclophilin | 1E6J(P) | HIV capsid | 1.33 | 1029 |
| 1AKJ(AB:DE) | O | 2CLR(DE) | MHC class 1 HLA-A2 | 1CD8(AB) | T-cell CD8 coreceptor | 1.14 | 1995 |
| 1B6C(A:B) | O | 1D6O(A) | FKBP-binding protein | 1IAS(A) | TGFβ receptor | 1.96 | 1752 |
| 1BUH(A:B) | O | 1HCL | CDK2 kinase | 1DKS(A) | Ckshs1 | 0.75 | 1324 |
| 1E96(A:B) | O | 1MH1 | Rac GTApase | 1HH8(A) | p67 Phox | 0.71 | 1179 |
| 1F51(AB:E) | O | 1IXM(AB) | Sporulation response factor B | 1SRR(C) | Sporulation response factor F | 0.74 | 2407 |
| 1FC2(C:D) | O | 1BDD | Staphylococcus protein A | 1FC1(AB) | Human Fc fragment | 1.69 | 1307 |
| 1FQJ(A:B) | O | 1TND(C) | Gt-α | 1FQI(A) | RGS9 | 0.91 | 1806 |
| 1GCQ(B:C) | O | 1GRI(B) | GRB2 C-ter SH3 domain | 1GCP(B) | GRB2 N-ter SH3 domain | 0.92 | 1208 |
| 1GHQ(A:B) | O | 1C3D | Epstein-Barr virus receptor CR2 | 1LY2(A) | Complement C3 | 0.34 | 800 |
| 1HE1(C:A) | O | 1MH1 | Rac GTPase | 1HE9(A) | Pseudomonas toxin GAP dom. | 0.93 | 2113 |
| 1I4D(D:AB) | O | 1MH1 | Rac GTPase | 1I49(AB) | Arfaptin | 1.41 | 1657 |
| 1KAC(A:B) | O | 1NOB(F) | Adenovirus fiber knob protein | 1F5W(B) | Adenovirus receptor | 0.95 | 1456 |
| 1KLU(AB:D) | O | 1H15(AB) | MHC class 2 HLA-DR1 | 1STE | Staphylococcus enterotoxin C3 | 0.43 | 1254 |
| 1KTZ(A:B) | O | 1TGK | TGF-β | 1M9Z(A) | TGF-β receptor | 0.39 | 989 |
| 1KXP(A:D) | O | 1IJJ(B) | Actin | 1KW2(B) | Vitamin D binding protein | 1.12 | 3341 |
| 1ML0(AB:D) | O | 1MKF(AB) | Viral chemokine binding p. M3 | 1DOL | Chemokine Mcp1 | 1.02 | 2069 |
| 1QA9(A:B) | O | 1HNF | CD2 | 1CCZ(A) | CD58 | 0.73 | 1353 |
| 1RLB(ABCD:E) | O | 2PAB(ABCD) | Transthyretin | 1HBP | Retinol binding protein | 0.66 | 1439 |
| 1SBB(A:B) | O | 1BEC | T-cell receptor β | 1SE4 | Staphylococcus enterotoxin B | 0.37 | 1064 |
| 2BTF(A:P) | O | 1IJJ(B) | Actin | 1PNE | Profilin | 0.75 | 2063 |
| 1BJ1(HL:VW) | AB | 1BJ1(HL) | FAB | 2VPF(GH) | vEGF | 0.50 | 1731 |
| 1FSK(BC:A) | AB | 1FSK(BC) | FAB | 1BV1 | Birch pollen antigen Bet V1 | 0.45 | 1623 |
| 1I9R(HL:ABC) | AB | 1I9R(HL) | FAB | 1ALY(ABC) | Cd40 ligand | 1.30 | 1498 |
| 1IQD(AB:C) | AB | 1IQD(AB) | FAB | 1D7P(M) | Factor VIII domain C2 | 0.48 | 1976 |
| 1K4C(AB:C) | AB | 1K4C(AB) | FAB | 1JVM(ABCD) | Potassium channel Kcsa | 0.53 | 1601 |
| 1KXQ(H:A) | AB | 1KXQ(H) | Camel VHH | 1PPI | Pancreatic α-amylase | 0.72 | 2172 |
| 1NCA(HL:N) | AB | 1NCA(HL) | FAB | 7NN9 | Flu virus neuraminidase N9 | 0.24 | 1953 |
| 1NSN(HL:S) | AB | 1NSN(HL) | FAB N10 | 1KDC | Staphylococcal nuclease | 0.35 | 1776 |
| 1QFW(HL:AB) | AB | 1QFW(HL) | Fv | 1HRP(AB) | Human chorionic gonadotropin | 1.31 | 1580 |
| 1QFW(IM:AB) | AB | 1QFW(IM) | Fv | 1HRP(AB) | Human chorionic gonadotropin | 0.73 | 1637 |
| 2JEL(HL:P) | AB | 2JEL(HL) | FAB Jel42 | 1POH | HPr | 0.17 | 1501 |
| Medium Difficulty (13) | |||||||
| 1ACB(E:I) | E | 2CGA(B) | Chymotrypsin | 1EGL | Eglin C | 2.26 | 1544 |
| 1KKL(ABC:H) | E | 1JB1(ABC) | HPr kinase C-ter domain | 2HPR | HPr | 2.20 | 1641 |
| 1BGX(HL:T) | A | 1AY1(HL) | FAB | 1CMW(A) | Taq polymerase | 1.48 | 5814 |
| 1GP2(A:BG) | O | 1GIA | Gi-α | 1TBG(DH) | Gi-βγ | 1.65 | 2287 |
| 1GRN(A:B) | O | 1A4R(A) | CDC42 GTPase | 1RGP | CDC42 GAP | 1.22 | 2332 |
| 1HE8(B:A) | O | 821P | Ras GTPase | 1E8Z(A) | PIP3 kinase | 0.92 | 1305 |
| 1I2M(A:B) | O | 1QG4(A) | Ran GTPase | 1A12(A) | RCC1 | 2.12 | 2779 |
| 1IB1(AB:E) | O | 1QJB(AB) | 14-3-3 protein | 1KUY(A) | Serotonin N-acteylase | 2.09 | 2808 |
| 1IJK(BC:A) | O | 1FVU(AB) | Botrocetin | 1AUQ | Von Willebrand factor dom. A1 | 0.68 | 1648 |
| 1K5D(AB:C) | O | 1RRP(AB) | Ran GTPase | 1YRG(B) | Ran GAP | 1.19 | 2527 |
| 1M10(A:B) | O | 1AUQ | Von Willebrand factor dom. A1 | 1MOZ(B) | Glycoprotein IB-α | 2.10 | 2097 |
| 1N2C(ABCD:EF) | O | 3MIN(ABCD) | Nitrogenase Mo-Fe protein | 2NIP(AB) | Nitrogenase Fe protein | 2.13 | 3635 |
| 1WQ1(R:G) | O | 6Q21(D) | Ras GTPase | 1WER | Ras GAP | 1.16 | 2913 |
| Difficult (8) | |||||||
| 1ATN(A:D) | O | 1IJJ(B) | Actin | 3DNI | Dnase I | 3.28 | 1774 |
| 1DE4(AB:CF) | O | 1A6Z(AB) | β2-microglobulin | 1CX8(AB) | Transferrin receptor ectodom | 2.59 | 2066 |
| 1EER(A:BC) | O | 1BUY(A) | Erythropoietin | 1ERN(AB) | EPO receptor | 2.44 | 3347 |
| 1FAK(HL:T) | O | 1QFK(HL) | Coagulation factor VIIa | 1TFH(B) | Soluble tissue factor | 6.18 | 3363 |
| 1FQ1(A:B) | O | 1FPZ(F) | CDK inhibitor 3 | 1B39(A) | CDK2 kinase | 3.41 | 1832 |
| 1H1V(A:G) | O | 1IJJ(B) | Actin | 1D0N(B) | Gelsolin | 6.62 | 2071 |
| 1IBR(A:B) | O | 1QG4(A) | Ran GTPase | 1F59(A) | Importin β | 2.54 | 3370 |
| 2HMI(CD:AB) | AB | 2HMI(CD) | FAB 28 | 1S6P(AB) | HIV1 reverse transcriptase | 2.26 | 1234 |
|
a Complex category labels: E, Enzyme Inhibitor or Enzyme Substrate; A, Antibody Antigen; O, Others; AB, Antigen Bound Antibody. | |||||||
Source: Benchmark 2.0[1]
Area
The area is the mean accessible surface area (ASA) buried by each chain in the pairwise complex:
area = [ (ASA(chain 1) + ASA(chain 2)) - ASA(pairwise complex) ] / 2
The accessible surface area can also be computed by the NSC program.[4]
See also
References
- ↑ 1.0 1.1 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.
- ↑ Méndez R, Leplae R, De Maria L, Wodak SJ (2003). Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins, 52:51-67.
- ↑ Hubbard SJ, Thornton JM (1993). NACCESS 2.1.1. Deptartment of Biochemistry and Molecular Biology, University College, London.
- ↑ Eisenhaber and Argos (1993). J Comput Chem, 11:1272-1280.
