Difference between revisions of "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<ref name=Minteris>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.
+
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.
  
 
== Benchmark table ==
 
== Benchmark table ==
−
<div style="float:left; margin:0px 20px 20px 0px;">
+
<div style="float:left; margin:0px 0px 0px 0px;">
 
{| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
 
{| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
 
|-
 
|-
−
! colspan="8" bgcolor="#EFEFEF" | '''Benchmarks'''
+
! colspan="8" bgcolor="#EFEFEF" | '''Protein Protein Docking Benchmark 2.0'''
−
|-align="center" style="background-color:#1188ee; color:#ffffff;"
+
|--align="center" style="background-color:#1188ee; color:#ffffff;"
−
!Complex<sup>a</sup>
+
!Complex
−
!Receptor<sup>a</sup>
+
!Cat.
−
!Ligand<sup>a</sup>
+
!PDBid 1
−
!Receptor description
+
!Protein 1
−
!Ligand description
+
!PDBid 2
−
!RMSD<sup>b</sup>(Å)
+
!Protein 2
−
!C&alpha;<sup>c</sup>
+
!RMSD<sup>b</sup> (Å)
−
!&Delta;ASA<sup>d</sup>(Å<sup>2</sup>)
+
!DASA<sup>c</sup> (Å<sup>2</sup>)
 
|-
 
|-
−
| colspan="8" bgcolor="#eeeeee" | '''Enzyme-inhibitor (22)'''
+
|-- colspan="8" bgcolor="#eeeeee" | '''Rigid-body (63)'''
 
|-
 
|-
−
| colspan="8" | Unbound-unbound (16)
+
| 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
 
|-
 
|-
−
| {{rcsb|1ACB|1ACB(E:I)}} || 5CHA(A) || 1CSE(I) || &alpha;-Chymotrypsin || Eglin C || align="right" | 0.7 || align="right" | 1 || align="right" | 1540
+
| colspan="8" bgcolor="#eeeeee" | '''Medium Difficulty (13)'''
 
|-
 
|-
−
| 1AVW(A:B) || 2PTN || 1BA7(A) || Trypsin || Soybean trypsin inhibitor || align="right" | 0.35 || align="right" | 0 || align="right" | 1740
+
| 1ACB(E:I)
−
|-
+
|| E
−
| 1BRC(E:I) || 1BRA || 1AAP(A) || Trypsin || APPI || align="right" | 0.44 || align="right" | 0 || align="right" | 1320
+
|| 2CGA(B)
−
|-
+
|| Chymotrypsin
−
| 1BRS(A:D) || 1A2P(B) || 1A19(A) || Barnase || Barstar || align="right" | 0.47 || align="right" | 0 || align="right" | 1560
+
|| 1EGL
−
|-
+
|| Eglin C
−
| 1CGI(E:I) || 1CHG || 1HPT || &alpha;-Chymotrypsinogen || Pancreatic secretory trypsin inhibitor || align="right" | 1.48 || align="right" | 14 || align="right" | 2050
+
| align="right" | 2.26
−
|-
+
| align="right" | 1544
−
| 1CHO(E:I) || 5CHA(A) || 2OVO || &alpha;-Chymotrypsin || Ovomucoid 3rd domain || align="right" | 0.59 || align="right" | 1 || align="right" | 1470
+
|-----
−
|-
+
| 1KKL(ABC:H)
−
| 1CSE(E:I) || 1SCD || 1ACB(I) || Subtilisin Carlsberg || Eglin C || align="right" | 0.43 || align="right" | 0 || align="right" | 1490
+
|| 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
 
|-
 
|-
−
| 1DFJ(I:E) || 2BNH || 7RSA || Ribonuclease inhibitor || Ribonuclease A || align="right" | 1.04 || align="right" | 13 || align="right" | 2580
+
| colspan="8" bgcolor="#eeeeee" | '''Difficult (8)'''
 
|-
 
|-
−
| IFSS(A:B) || 2ACE(E) || 1FSC || Snake venom acetylcholinesterase || Fasciculin II || align="right" | 0.75 || align="right" | 1 || align="right" | 1970
+
| 1ATN(A:D)
−
|-
+
|| O
−
| 1MAH(A:F) || 1MAA(B) || 1FSC || Mouse acetylcholinesterase || Fasciculin II || align="right" | 0.6 || align="right" | 0 || align="right" | 2150
+
|| 1IJJ(B)
−
|-
+
|| Actin
−
| 1TGS(Z:I) || 2PTN || 1HPT || Trypsinogen || Pancreatic secretory trypsin inhibitor || align="right" | 1.49 || align="right" | 17 || align="right" | 1720
+
|| 3DNI
−
|-
+
|| Dnase I
−
| 1UGH(E:I) || 1AKZ || 1UGI(A) || Human Uracil-DNA glycosylase || Inhibitor || align="right" | 0.53 || align="right" | 1 || align="right" | 2190
+
| align="right" | 3.28
−
|-
+
| align="right" | 1774
−
| 2KAI(AB:I) || 2PKA(XY) || 6PTI || Kallikrein A || Trypsin inhibitor || align="right" | 0.7 || align="right" | 2 || align="right" | 1420
+
−
|-
+
−
| 2PTC(E:I) || 2PTN || 6PTI || &beta;-Trypsin || Pancreatic trypsin inhibitor || align="right" | 0.32 || align="right" | 0 || align="right" | 1430
+
−
|-
+
−
| 2SIC(E:I) || 1SUP || 3SSI || Subtilisin BPN || Subtilisin inhibitor || align="right" | 0.4 || align="right" | 0 || align="right" | 1620
+
−
|-
+
−
| 2SNI(E:I) || 1SUP || 2C12(I) || Subtilisin Novo || Chymotrypsin inhibitor 2 || align="right" | 0.37 || align="right" | 0 || align="right" | 1630
+
−
|-
+
−
| colspan="8" | Unbound-bound (6)
+
−
|-
+
−
| 1PPE(E:I) || 2PTN || 1PPE(I) || Trypsin || CMT-I || align="right" | 0.27 || align="right" | 0 || align="right" | 1690
+
−
|-
+
−
| 1STF(E:I) || 1PPN || 1STF(I) || Papain || Stefin B || align="right" | 0.25 || align="right" | 0 || align="right" | 1790
+
−
|-
+
−
| 1TAB(E:I) || 2PTN || 1TAB(I) || Trypsin || BBI || align="right" | 0.27 || align="right" | 0 || align="right" | 1360
+
−
|-
+
−
| 1UDI(E:I) || 1UDH || 1UDI(I) || Virus Uracil-DNA glycosylase || Inhibitor || align="right" | 0.36 || align="right" | 0 || align="right" | 2020
+
−
|-
+
−
| 2TEC(E:I) || 1THM || 2TEC(I) || Thermitase || Eglin C || align="right" | 0.19 || align="right" | 0 || align="right" | 1560
+
−
|-
+
−
| 4HTC(LH:I) || 2HNT(LCEF) || 4HTC(I) || A-Thrombin || Hirudin || align="right" | 0.56 || align="right" | 2 || align="right" | 3320
+
−
|-
+
−
| colspan="8" bgcolor="#eeeeee" | '''Antibody-antigen (19)'''
+
−
|-
+
−
| colspan="8" | Unbound-unbound (5)
+
−
|-
+
−
| 1AHW(DE:F) || 1FGN(LH) || 1BOY || Antibody Fab 5G9 || Tissue factor || align="right" | 0.71 || align="right" | 1 || align="right" | 1900
+
−
|-
+
−
| 1BVK(DE:F) || 1BVL(LH) || 3LZT || Antibody Hulysll Fv || Lysozyme || align="right" | 1.22 || align="right" | 3 || align="right" | 1400
+
−
|-
+
−
| 1DQJ(AB:C) || 1DQQ(LH) || 3LZT || Hyhel-63 Fab || Lysozyme || align="right" | 0.73 || align="right" | 3 || align="right" | 1760
+
−
|-
+
−
| 1MLC(AB:E) || 1MLB(AB) || 1LZA || IgG1 D44.1 Fab fragment || Lysozyme || align="right" | 0.85 || align="right" | 3 || align="right" | 1390
+
−
|-
+
−
| 1WEJ(LH:F) || 1QBL(LH) || 1HRC || IgG1 E8 Fab fragment || Cytochrome C || align="right" | 0.32 || align="right" | 0 || align="right" | 1180
+
−
|- colspan="8" | Unbound-bound (14)
+
−
| 1BQL(LH:Y) || 1BQL(LH) || 1DKJ || Hyhel-5 Fab || Lysozyme || align="right" | 0.52 || align="right" | 2 || align="right" | 1630
+
−
|-
+
−
| 1EO8(LH:A) || 1EO8(LH) || 2VIU(A) || Bh151 Fab || Influenza virus hemagglutinin || align="right" | 0.28 || align="right" | 0 || align="right" | 1530
+
−
|-
+
−
| 1FBI(LH:X) || 1FBI(LH) || 1HHL || IgG1 Fab fragment || Lysozyme || align="right" | 0.5 || align="right" | 0 || align="right" | 1690
+
−
|-
+
−
| 1IAI(MI:LH) || 1AIF(LH) || 1IAI(LH) || IgG1 Idiotypic Fab || Igg2A anti-idiotypic Fab || align="right" | 0.99 || align="right" | 12 || align="right" | 1890
+
−
|-
+
−
| 1JHL(LH:A) || 1JHL(LH) || 1GHL(A) || IgG1 Fv fragment || Lysozyme || align="right" | 0.26 || align="right" | 0 || align="right" | 1240
+
−
|-
+
−
| 1KXQ(D:E) || 1PIF(A) || 1KXQ(E) || &alpha;-Amylase || Camelid AMD9 Vhh domain || align="right" | 0.43 || align="right" | 0 || align="right" | 2140
+
−
|-
+
−
| 1KXT(A:B) || 1PIF(A) || 1KXT(B) || &alpha;-Amylase || Camelid AMB7 Vhh domain || align="right" | 0.39 || align="right" | 0 || align="right" | 1620
+
−
|-
+
−
| 1KXV(A:C) || 1PIF(A) || 1KXV(C) || &alpha;-Amylase || Camelid AMD10 Vhh domain || align="right" | 0.24 || align="right" | 0 || align="right" | 1620
+
−
|-
+
−
| 1MEL(B:M) || 1MEL(B) || 1LZA || Vh single-domain antibody || Lysozyme || align="right" | 0.65 || align="right" | 2 || align="right" | 1690
+
−
|-
+
−
| 1NCA(LH:N) || 1NCA(LH) || 7NN9 || Fab NC41 || Influenza virus neuraminidase || align="right" | 0.24 || align="right" | 0 || align="right" | 1950
+
−
|-
+
−
| 1NMB(LH:N) || 1NMB(LH) || 7NN9 || Fab NC10 || Influenza virus neuraminidase || align="right" | 0.21 || align="right" | 0 || align="right" | 1350
+
−
|-
+
−
| 1QFU(LH:A) || 1QFU(LH) || 2VIU(A) || Igg1-k Fab || Influenza virus hemagglutinin || align="right" | 0.27 || align="right" | 0 || align="right" | 1840
+
−
|-
+
−
| 2JEL(LH:P) || 2JEL(LH) || 1POH || Jel42 Fab fragment || A06 phosphotransferase || align="right" | 0.18 || align="right" | 0 || align="right" | 1500
+
−
|-
+
−
| 2VIR(AB:C) || 2VIR(AB) || 2VIU(A) || Igg1-lamda Fab || Influenza virus hemagglutinin || align="right" | 0.41 || align="right" | 1 || align="right" | 1260
+
−
|-
+
−
| colspan="8" bgcolor="#eeeeee" | '''Others (11)'''
+
−
|-
+
−
| colspan="8" | Unbound-unbound (5)
+
−
|-
+
−
| 1AVZ(B:C) || 1AVV || 1SHF(A) || HIV-1 NEF || FYN tyrosin kinase SH3 domain || align="right" | 0.73 || align="right" | 1 || align="right" | 1260
+
−
|-
+
−
| 1L0Y(A:B) || 1BEC || 1B1Z(A) || T-cell receptor &beta; chain || Exotoxin A1 || align="right" | 0.83 || align="right" | 2 || align="right" | 1130
+
−
|-
+
−
| 1WQ1(G:R) || 1WER || 5P21 || RAS activating domain || RAS || align="right" | 0.83 || align="right" | 9 || align="right" | 2910
+
−
|-
+
−
| 2MTA(LH:A) || 2BBK(LH) || 1AAN || Methylamine dehydrogenase || Amicyanin || align="right" | 0.34 || align="right" | 0 || align="right" | 1460
+
−
|-
+
−
| 2PCC(A:B) || 1CCA || 1YCC || Cytochrome C peroxidase || Iso-1-Cytochrome C || align="right" | 0.44 || align="right" | 1 || align="right" | 1140
+
−
|-
+
−
| colspan="8" | Unbound-bound (6)
+
−
|-
+
−
| 1A0O(A:B) || 1CHN || 1A0O(B) || Che A || Che Y || align="right" | 1.59 || align="right" | 9 || align="right" | 1130
+
−
|-
+
−
| 1ATN(A:D) || 1ATN(A) || 3DNI || Actin || Deoxyribonuclease I || align="right" | 0.31 || align="right" | 0 || align="right" | 1770
+
−
|-
+
−
| 1GLA(G:F) || 1GLA(G) || 1F3G || Glycerol kinase || GSF III || align="right" | 0.37 || align="right" | 0 || align="right" | 1300
+
−
|-
+
−
| 1IGC(LH:A) || 1IGC(LH) || 1IGD || IgG1 Fab fragment || Protein G || align="right" | 0.74 || align="right" | 1 || align="right" | 1330
+
−
|-
+
−
| 1SPB(S:P) || 1SUP || 1SPB(P) || Subtilisin || Subtilisin prosegment || align="right" | 0.35 || align="right" | 0 || align="right" | 2230
+
−
|-
+
−
| 2BTF(A:P) || 2BTF(A) || 1PNE || &beta;-Actin || Profilin || align="right" | 0.29 || align="right" | 0 || align="right" | 2060
+
−
|-
+
−
| colspan="8" bgcolor="#eeeeee" | '''Difficult test cases (7)'''
+
−
|-
+
−
| colspan="8" | Unbound-unbound (5)
+
−
|-
+
−
| 1BTH(LH:P) || 2HNT(LCEF) || 6PTI || Thrombin mutant || Pancreatic trypsin inhibitor || align="right" | 1.91 || align="right" | 18 || align="right" | 2370
+
−
|-
+
−
| 1FIN(A:B) || 1HCL || 1VIN || CDK2 cyclindependant kinase 2 || Cyclin || align="right" | 4.66 || align="right" | 59 || align="right" | 3400
+
−
|-
+
−
| 1FQ1(B:A) || 1B39(A) || 1FPZ(F) || CDK2 || KAP || align="right" | 3.55 || align="right" | 23 || align="right" | 1830
+
−
|-
+
−
| 1GOT(A:BG) || 1TAG || 1TBG(AE) || Transducin Gt-&alpha;, Gi-&alpha; chimera || Gt-&beta;-&gamma; || align="right" | 2.45 || align="right" | 30 || align="right" | 2500
+
−
|-
+
−
| 1KKL(AC:H) || 1JB1 || 1SPH(A) || HPr kinase || Phosphocarrier protein Hpr || align="right" | 2.53 || align="right" | 28 || align="right" | 1640
+
−
|-
+
−
| colspan="8" | Unbound-bound (2)
+
−
|-
+
−
| 1EFU(A:B) || 1D8T(A) || 1EFU(B) || ''E. coli'' Ef-Tu || Efts || align="right" | 2.57 || align="right" | 109 || align="right" | 3630
+
−
|-
+
−
| 3HHR(B:A) || 3HHR(B) || 1HGU || Human growth hormone || Receptor || align="right" | 2.04 || align="right" | 24 || align="right" | 4150
+
 
|-----
 
|-----
−
|colspan="8" style="border-top: 1px solid #333;"|<small>'''a''' Four-letter PDB code for the crystal structures used in this study with chain IDs in parenthesis.
+
| 1DE4(AB:CF)
−
'''b''' The RMSD of the interface C&alpha; atoms for input receptor and ligand after superposition onto the co-crystallized complex structure, calculated as in our previous work.<ref>Chen R, Weng Z (2002). Docking unbound proteins using shape complementarity, desolvation, and electrostatics. ''Proteins, 47:281-294''.</ref><br/>
+
|| O
−
'''c''' Number of interface C&alpha; atoms with RMSD larger than 2Å between unbound and bound structures after superposition.<br/>
+
|| 1A6Z(AB)
−
'''d''' &Delta;ASA: change in accessible surface area (ASA) on complex formation was calculated, by using the program NACCESS.<ref>Hubbard SJ, Thornton JM (1993). NACCESS. ''University College London: Department of Biochemistry and Molecular Biology''.</ref></small>
+
|| &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>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 NACCESS.<ref>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 1.0<ref>Chen R, Mintseris J, Janin J, Weng Z (2003). A protein-protein docking benchmark. ''Proteins: Structure, Function, and Genetics, 52:88-91''.</ref>''</div>
+
<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>
 
</div>
−
 
 
== References ==
 
== References ==
 
<references/>
 
<references/>
  
 
[[Category:Academic Research]]
 
[[Category:Academic Research]]

Revision as of 02:28, 30 September 2006

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

Protein Protein Docking Benchmark 2.0
Complex Cat. PDBid 1 Protein 1 PDBid 2 Protein 2 RMSDb (Å) DASAc (Å2)
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.
b RMSD of Cα atoms of interface residues calculated as described previously,[2] after finding the best superposition of bound and unbound interfaces.
c Change in accessible surface area upon complex formation calculated using NACCESS.[3]

Source: Benchmark 2.0[1]

References

  1. ↑ 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.
  2. ↑ 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.
  3. ↑ Hubbard SJ, Thornton JM (1993). NACCESS 2.1.1. Deptartment of Biochemistry and Molecular Biology, University College, London.
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