View source for Protein-Protein Docking Benchmark

A benchmark of 84 protein-protein interactions with known complexed structures has been developed for testing docking methods<ref name="Mintseris">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''.</ref>. 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 [http://scop.mrc-lmb.cam.ac.uk/scop/ 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 [http://zlab.bu.edu/julianm/benchmark/ Supplementary Information]

==Protein-Protein Docking Benchmark 2.0==
<div style="float:left; margin:0px 0px 0px 0px;">
{| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
|-
! colspan="8" bgcolor="#EFEFEF" | '''Protein-Protein Docking Benchmark 2.0'''
|--align="center" style="background-color:#1188ee; color:#ffffff;"
!Complex
!Cat.<sup>a</sup>
!PDBid 1
!Protein 1
!PDBid 2
!Protein 2
!RMSD<sup>b</sup> (Å)
!DASA<sup>c</sup> (Å<sup>2</sup>)
|-
| colspan="8" bgcolor="#eeeeee" | '''Rigid-body (63)'''
|-
| 1AVX(A:B)
|| E
|| 1QQU(A)
|| Porcine trypsin
|| 1BA7(B)
|| Soybean trypsin inhibitor
| align="right" | 0.47
| align="right" | 1585
|-----
| 1AY7(A:B)
|| E
|| 1RGH(B)
|| Barnase
|| 1A19(B)
|| Barstar
| align="right" | 0.54
| align="right" | 1237
|-----
| 1BVN(P:T)
|| E
|| 1PIG
|| &alpha;-amylase
|| 1HOE
|| Tendamistat
| align="right" | 0.87
| align="right" | 2222
|-----
| 1CGI(E:I)
|| E
|| 2CGA(B)
|| Bovine chymotrypsinogen
|| 1HPT
|| PSTI
| align="right" | 2.02
| align="right" | 2053
|-----
| 1D6R(A:I)
|| E
|| 2TGT
|| Bovine trypsin
|| 1K9B(A)
|| Bowman&ndash;Birk inhibitor
| align="right" | 1.14
| align="right" | 1408
|-----
| 1DFJ(E:I)
|| E
|| 9RSA(B)
|| Ribonuclease A
|| 2BNH
|| Rnase inhibitor
| align="right" | 1.02
| align="right" | 2582
|-----
| 1E6E(A:B)
|| E
|| 1E1N(A)
|| Adrenoxin reductase
|| 1CJE(D)
|| Adrenoxin
| align="right" | 1.33
| align="right" | 2315
|-----
| 1EAW(A:B)
|| E
|| 1EAX(A)
|| Matriptase
|| 9PTI
|| BPTI
| align="right" | 0.54
| align="right" | 1866
|-----
| 1EWY(A:C)
|| E
|| 1GJR(A)
|| Ferredoxin reductase
|| 1CZP(A)
|| Ferredoxin
| align="right" | 0.80
| align="right" | 1502
|-----
| 1EZU(C:AB)
|| E
|| 1TRM(A)
|| D102N trypsin
|| 1ECZ(AB)
|| Ecotin
| align="right" | 1.21
| align="right" | 2751
|-----
| 1F34(A:B)
|| E
|| 4PEP
|| Porcine pepsin
|| 1F32(A)
|| Ascaris inhibitor 3
| align="right" | 0.93
| align="right" | 3038
|-----
| 1HIA(AB:I)
|| E
|| 2PKA(XY)
|| Kallikrein
|| 1BXB
|| Hirustatin
| align="right" | 1.40
| align="right" | 1737
|-----
| 1MAH(A:F)
|| E
|| 1J06(B)
|| Acetylcholinesterase
|| 1FSC
|| Fasciculin
| align="right" | 0.61
| align="right" | 2145
|-----
| 1PPE(E:I)
|| E
|| 1BTP
|| Bovine trypsin
|| 1LU0(A)
|| CMTI-1 squash inhibitor
| align="right" | 0.44
| align="right" | 1688
|-----
| 1TMQ(A:B)
|| E
|| 1JAE
|| &alpha;-amylase
|| 1B1U(A)
|| RAGI inhibitor
| align="right" | 0.86
| align="right" | 2401
|-----
| 1UDI(E:I)
|| E
|| 1UDH
|| Uracyl-DNA glycosylase
|| 2UGI(B)
|| Glycosylase inhibitor
| align="right" | 0.90
| align="right" | 2022
|-----
| 2MTA(HL:A)
|| E
|| 2BBK(JM)
|| Methylamine dehydrogenase
|| 2RAC(A)
|| Amicyanin
| align="right" | 0.41
| align="right" | 1461
|-----
| 2PCC(A:B)
|| E
|| 1CCP
|| Cyt C peroxidase
|| 1YCC
|| Cytochrome C
| align="right" | 0.39
| align="right" | 1141
|-----
| 2SIC(E:I)
|| E
|| 1SUP
|| Subtilisin
|| 3SSI
|| Streptomyces subtilisin inhibitor
| align="right" | 0.36
| align="right" | 1617
|-----
| 2SNI(E:I)
|| E
|| 1UBN(A)
|| Subtilisin
|| 2CI2(I)
|| Chymotrypsin inhibitor 2
| align="right" | 0.35
| align="right" | 1628
|-----
| 7CEI(A:B)
|| E
|| 1UNK(D)
|| Colicin E7 nuclease
|| 1M08(B)
|| Im7 immunity protein
| align="right" | 0.70
| align="right" | 1384
|-----
| 1AHW(AB:C)
|| A
|| 1FGN(LH)
|| Fab 5g9
|| 1TFH(A)
|| Tissue factor
| align="right" | 0.69
| align="right" | 1899
|-----
| 1BVK(DE:F)
|| A
|| 1BVL(BA)
|| Fv Hulys11
|| 3LZT
|| HEW lysozyme
| align="right" | 1.24
| align="right" | 1321
|-----
| 1DQJ(AB:C)
|| A
|| 1DQQ(CD)
|| FAB Hyhel63
|| 3LZT
|| HEW lysozyme
| align="right" | 0.75
| align="right" | 1765
|-----
| 1E6J(HL:P)
|| A
|| 1E6O(HL)
|| FAB
|| 1A43
|| HIV-1 capsid protein p24
| align="right" | 1.05
| align="right" | 1245
|-----
| 1JPS(HL:T)
|| A
|| 1JPT(HL)
|| FAB D3H44
|| 1TFH(B)
|| Tissue factor
| align="right" | 0.51
| align="right" | 1852
|-----
| 1MLC(AB:E)
|| A
|| 1MLB(AB)
|| FAB44.1
|| 3LZT
|| HEW lysozyme
| align="right" | 0.60
| align="right" | 1392
|-----
| 1VFB(AB:C)
|| A
|| 1VFA(AB)
|| Fv D1.3
|| 8LYZ
|| HEW lysozyme
| align="right" | 1.02
| align="right" | 1383
|-----
| 1WEJ(HL:F)
|| A
|| 1QBL(HL)
|| FAB E8
|| 1HRC
|| Cytochrome C
| align="right" | 0.31
| align="right" | 1177
|-----
| 2VIS(AB:C)
|| A
|| 1GIG(LH)
|| FAB
|| 2VIU(ACE)
|| Flu virus hemagglutinin
| align="right" | 0.80
| align="right" | 1296
|-----
| 1A2K(C:AB)
|| O
|| 1QG4(A)
|| Ran GTPase
|| 1OUN(AB)
|| Nuclear transport factor 2
| align="right" | 1.11
| align="right" | 1603
|-----
| 1AK4(A:D)
|| O
|| 2CPL
|| Cyclophilin
|| 1E6J(P)
|| HIV capsid
| align="right" | 1.33
| align="right" | 1029
|-----
| 1AKJ(AB:DE)
|| O
|| 2CLR(DE)
|| MHC class 1 HLA-A2
|| 1CD8(AB)
|| T-cell CD8 coreceptor
| align="right" | 1.14
| align="right" | 1995
|-----
| 1B6C(A:B)
|| O
|| 1D6O(A)
|| FKBP-binding protein
|| 1IAS(A)
|| TGF&beta; receptor
| align="right" | 1.96
| align="right" | 1752
|-----
| 1BUH(A:B)
|| O
|| 1HCL
|| CDK2 kinase
|| 1DKS(A)
|| Ckshs1
| align="right" | 0.75
| align="right" | 1324
|-----
| 1E96(A:B)
|| O
|| 1MH1
|| Rac GTApase
|| 1HH8(A)
|| p67 Phox
| align="right" | 0.71
| align="right" | 1179
|-----
| 1F51(AB:E)
|| O
|| 1IXM(AB)
|| Sporulation response factor B
|| 1SRR(C)
|| Sporulation response factor F
| align="right" | 0.74
| align="right" | 2407
|-----
| 1FC2(C:D)
|| O
|| 1BDD
|| Staphylococcus protein A
|| 1FC1(AB)
|| Human Fc fragment
| align="right" | 1.69
| align="right" | 1307
|-----
| 1FQJ(A:B)
|| O
|| 1TND(C)
|| Gt-&alpha;
|| 1FQI(A)
|| RGS9
| align="right" | 0.91
| align="right" | 1806
|-----
| 1GCQ(B:C)
|| O
|| 1GRI(B)
|| GRB2 C-ter SH3 domain
|| 1GCP(B)
|| GRB2 N-ter SH3 domain
| align="right" | 0.92
| align="right" | 1208
|-----
| 1GHQ(A:B)
|| O
|| 1C3D
|| Epstein-Barr virus receptor CR2
|| 1LY2(A)
|| Complement C3
| align="right" | 0.34
| align="right" | 800
|-----
| 1HE1(C:A)
|| O
|| 1MH1
|| Rac GTPase
|| 1HE9(A)
|| Pseudomonas toxin GAP dom.
| align="right" | 0.93
| align="right" | 2113
|-----
| 1I4D(D:AB)
|| O
|| 1MH1
|| Rac GTPase
|| 1I49(AB)
|| Arfaptin
| align="right" | 1.41
| align="right" | 1657
|-----
| 1KAC(A:B)
|| O
|| 1NOB(F)
|| Adenovirus fiber knob protein
|| 1F5W(B)
|| Adenovirus receptor
| align="right" | 0.95
| align="right" | 1456
|-----
| 1KLU(AB:D)
|| O
|| 1H15(AB)
|| MHC class 2 HLA-DR1
|| 1STE
|| Staphylococcus enterotoxin C3
| align="right" | 0.43
| align="right" | 1254
|-----
| 1KTZ(A:B)
|| O
|| 1TGK
|| TGF-&beta;
|| 1M9Z(A)
|| TGF-&beta; receptor
| align="right" | 0.39
| align="right" | 989
|-----
| 1KXP(A:D)
|| O
|| 1IJJ(B)
|| Actin
|| 1KW2(B)
|| Vitamin D binding protein
| align="right" | 1.12
| align="right" | 3341
|-----
| 1ML0(AB:D)
|| O
|| 1MKF(AB)
|| Viral chemokine binding p. M3
|| 1DOL
|| Chemokine Mcp1
| align="right" | 1.02
| align="right" | 2069
|-----
| 1QA9(A:B)
|| O
|| 1HNF
|| CD2
|| 1CCZ(A)
|| CD58
| align="right" | 0.73
| align="right" | 1353
|-----
| 1RLB(ABCD:E)
|| O
|| 2PAB(ABCD)
|| Transthyretin
|| 1HBP
|| Retinol binding protein
| align="right" | 0.66
| align="right" | 1439
|-----
| 1SBB(A:B)
|| O
|| 1BEC
|| T-cell receptor &beta;
|| 1SE4
|| Staphylococcus enterotoxin B
| align="right" | 0.37
| align="right" | 1064
|-----
| 2BTF(A:P)
|| O
|| 1IJJ(B)
|| Actin
|| 1PNE
|| Profilin
| align="right" | 0.75
| align="right" | 2063
|-----
| 1BJ1(HL:VW)
|| AB
|| 1BJ1(HL)
|| FAB
|| 2VPF(GH)
|| vEGF
| align="right" | 0.50
| align="right" | 1731
|-----
| 1FSK(BC:A)
|| AB
|| 1FSK(BC)
|| FAB
|| 1BV1
|| Birch pollen antigen Bet V1
| align="right" | 0.45
| align="right" | 1623
|-----
| 1I9R(HL:ABC)
|| AB
|| 1I9R(HL)
|| FAB
|| 1ALY(ABC)
|| Cd40 ligand
| align="right" | 1.30
| align="right" | 1498
|-----
| 1IQD(AB:C)
|| AB
|| 1IQD(AB)
|| FAB
|| 1D7P(M)
|| Factor VIII domain C2
| align="right" | 0.48
| align="right" | 1976
|-----
| 1K4C(AB:C)
|| AB
|| 1K4C(AB)
|| FAB
|| 1JVM(ABCD)
|| Potassium channel Kcsa
| align="right" | 0.53
| align="right" | 1601
|-----
| 1KXQ(H:A)
|| AB
|| 1KXQ(H)
|| Camel VHH
|| 1PPI
|| Pancreatic &alpha;-amylase
| align="right" | 0.72
| align="right" | 2172
|-----
| 1NCA(HL:N)
|| AB
|| 1NCA(HL)
|| FAB
|| 7NN9
|| Flu virus neuraminidase N9
| align="right" | 0.24
| align="right" | 1953
|-----
| 1NSN(HL:S)
|| AB
|| 1NSN(HL)
|| FAB N10
|| 1KDC
|| Staphylococcal nuclease
| align="right" | 0.35
| align="right" | 1776
|-----
| 1QFW(HL:AB)
|| AB
|| 1QFW(HL)
|| Fv
|| 1HRP(AB)
|| Human chorionic gonadotropin
| align="right" | 1.31
| align="right" | 1580
|-----
| 1QFW(IM:AB)
|| AB
|| 1QFW(IM)
|| Fv
|| 1HRP(AB)
|| Human chorionic gonadotropin
| align="right" | 0.73
| align="right" | 1637
|-----
| 2JEL(HL:P)
|| AB
|| 2JEL(HL)
|| FAB Jel42
|| 1POH
|| HPr
| align="right" | 0.17
| align="right" | 1501
|-
| colspan="8" bgcolor="#eeeeee" | '''Medium Difficulty (13)'''
|-
| 1ACB(E:I)
|| E
|| 2CGA(B)
|| Chymotrypsin
|| 1EGL
|| Eglin C
| align="right" | 2.26
| align="right" | 1544
|-----
| 1KKL(ABC:H)
|| E
|| 1JB1(ABC)
|| HPr kinase C-ter domain
|| 2HPR
|| HPr
| align="right" | 2.20
| align="right" | 1641
|-----
| 1BGX(HL:T)
|| A
|| 1AY1(HL)
|| FAB
|| 1CMW(A)
|| Taq polymerase
| align="right" | 1.48
| align="right" | 5814
|-----
| 1GP2(A:BG)
|| O
|| 1GIA
|| Gi-&alpha;
|| 1TBG(DH)
|| Gi-&beta;&gamma;
| align="right" | 1.65
| align="right" | 2287
|-----
| 1GRN(A:B)
|| O
|| 1A4R(A)
|| CDC42 GTPase
|| 1RGP
|| CDC42 GAP
| align="right" | 1.22
| align="right" | 2332
|-----
| 1HE8(B:A)
|| O
|| 821P
|| Ras GTPase
|| 1E8Z(A)
|| PIP3 kinase
| align="right" | 0.92
| align="right" | 1305
|-----
| 1I2M(A:B)
|| O
|| 1QG4(A)
|| Ran GTPase
|| 1A12(A)
|| RCC1
| align="right" | 2.12
| align="right" | 2779
|-----
| 1IB1(AB:E)
|| O
|| 1QJB(AB)
|| 14-3-3 protein
|| 1KUY(A)
|| Serotonin N-acteylase
| align="right" | 2.09
| align="right" | 2808
|-----
| 1IJK(BC:A)
|| O
|| 1FVU(AB)
|| Botrocetin
|| 1AUQ
|| Von Willebrand factor dom. A1
| align="right" | 0.68
| align="right" | 1648
|-----
| 1K5D(AB:C)
|| O
|| 1RRP(AB)
|| Ran GTPase
|| 1YRG(B)
|| Ran GAP
| align="right" | 1.19
| align="right" | 2527
|-----
| 1M10(A:B)
|| O
|| 1AUQ
|| Von Willebrand factor dom. A1
|| 1MOZ(B)
|| Glycoprotein IB-&alpha;
| align="right" | 2.10
| align="right" | 2097
|-----
| 1N2C(ABCD:EF)
|| O
|| 3MIN(ABCD)
|| Nitrogenase Mo-Fe protein
|| 2NIP(AB)
|| Nitrogenase Fe protein
| align="right" | 2.13
| align="right" | 3635
|-----
| 1WQ1(R:G)
|| O
|| 6Q21(D)
|| Ras GTPase
|| 1WER
|| Ras GAP
| align="right" | 1.16
| align="right" | 2913
|-
| colspan="8" bgcolor="#eeeeee" | '''Difficult (8)'''
|-
| 1ATN(A:D)
|| O
|| 1IJJ(B)
|| Actin
|| 3DNI
|| Dnase I
| align="right" | 3.28
| align="right" | 1774
|-----
| 1DE4(AB:CF)
|| O
|| 1A6Z(AB)
|| &beta;2-microglobulin
|| 1CX8(AB)
|| Transferrin receptor ectodom
| align="right" | 2.59
| align="right" | 2066
|-----
| 1EER(A:BC)
|| O
|| 1BUY(A)
|| Erythropoietin
|| 1ERN(AB)
|| EPO receptor
| align="right" | 2.44
| align="right" | 3347
|-----
| 1FAK(HL:T)
|| O
|| 1QFK(HL)
|| Coagulation factor VIIa
|| 1TFH(B)
|| Soluble tissue factor
| align="right" | 6.18
| align="right" | 3363
|-----
| 1FQ1(A:B)
|| O
|| 1FPZ(F)
|| CDK inhibitor 3
|| 1B39(A)
|| CDK2 kinase
| align="right" | 3.41
| align="right" | 1832
|-----
| 1H1V(A:G)
|| O
|| 1IJJ(B)
|| Actin
|| 1D0N(B)
|| Gelsolin
| align="right" | 6.62
| align="right" | 2071
|-----
| 1IBR(A:B)
|| O
|| 1QG4(A)
|| Ran GTPase
|| 1F59(A)
|| Importin &beta;
| align="right" | 2.54
| align="right" | 3370
|-----
| 2HMI(CD:AB)
|| AB
|| 2HMI(CD)
|| FAB 28
|| 1S6P(AB)
|| HIV1 reverse transcriptase
| align="right" | 2.26
| align="right" | 1234
|-----
|colspan="8" style="border-top: 1px solid #333;"|<small>
'''a''' Complex category labels: E, Enzyme Inhibitor or Enzyme Substrate; A, Antibody Antigen; O, Others; AB, Antigen Bound Antibody.<br/>
'''b''' RMSD of C&alpha; atoms of interface residues calculated as described previously,<ref name="Mendez">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''.</ref> after finding the best superposition of bound and unbound interfaces.<br/>
'''c''' Change in accessible surface area upon complex formation calculated using [http://wolf.bms.umist.ac.uk/naccess/ NACCESS].<ref name="Hubbard">Hubbard SJ, Thornton JM (1993). NACCESS 2.1.1. ''Deptartment of Biochemistry and Molecular Biology, University College, London''.</ref></small>
|}
<div align="center">''Source: Benchmark 2.0<ref name="Mintseris">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''.</ref>''</div>
</div>
<br clear="all"/>
==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.<ref name="Eisenhaber">Eisenhaber and Argos (1993). ''J Comput Chem, 11:1272-1280''.</ref>

==See also==
*[[Protein-Protein Docking Benchmark 1.0]]

==References==
<references/>

[[Category:Academic Research]]
[[Category:Bioinformatics]]