View source for Protein-Protein Docking Benchmark 1.0

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! colspan="8" bgcolor="#EFEFEF" | '''Benchmarks'''
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!Complex<sup>a</sup>
!Receptor<sup>a</sup>
!Ligand<sup>a</sup>
!Receptor description
!Ligand description
!RMSD<sup>b</sup>(Å)
!C&alpha;<sup>c</sup>
!&Delta;ASA<sup>d</sup>(Å<sup>2</sup>)
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| colspan="8" bgcolor="#eeeeee" | '''Enzyme-inhibitor (22)'''
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| colspan="8" | Unbound-unbound (16)
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| {{rcsb|1ACB|1ACB(E:I)}} || 5CHA(A) || 1CSE(I) || &alpha;-Chymotrypsin || Eglin C || align="right" | 0.7 || align="right" | 1 || align="right" | 1540
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| 1AVW(A:B) || 2PTN || 1BA7(A) || Trypsin || Soybean trypsin inhibitor || align="right" | 0.35 || align="right" | 0 || align="right" | 1740
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| 1BRC(E:I) || 1BRA || 1AAP(A) || Trypsin || APPI || align="right" | 0.44 || align="right" | 0 || align="right" | 1320
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| 1BRS(A:D) || 1A2P(B) || 1A19(A) || Barnase || Barstar || align="right" | 0.47 || align="right" | 0 || align="right" | 1560
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| 1CGI(E:I) || 1CHG || 1HPT || &alpha;-Chymotrypsinogen || Pancreatic secretory trypsin inhibitor || align="right" | 1.48 || align="right" | 14 || align="right" | 2050
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| 1CHO(E:I) || 5CHA(A) || 2OVO || &alpha;-Chymotrypsin || Ovomucoid 3rd domain || align="right" | 0.59 || align="right" | 1 || align="right" | 1470
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| 1CSE(E:I) || 1SCD || 1ACB(I) || Subtilisin Carlsberg || Eglin C || align="right" | 0.43 || align="right" | 0 || align="right" | 1490
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| 1DFJ(I:E) || 2BNH || 7RSA || Ribonuclease inhibitor || Ribonuclease A || align="right" | 1.04 || align="right" | 13 || align="right" | 2580
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| IFSS(A:B) || 2ACE(E) || 1FSC || Snake venom acetylcholinesterase || Fasciculin II || align="right" | 0.75 || align="right" | 1 || align="right" | 1970
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| 1MAH(A:F) || 1MAA(B) || 1FSC || Mouse acetylcholinesterase || Fasciculin II || align="right" | 0.6 || align="right" | 0 || align="right" | 2150
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| 1TGS(Z:I) || 2PTN || 1HPT || Trypsinogen || Pancreatic secretory trypsin inhibitor || align="right" | 1.49 || align="right" | 17 || align="right" | 1720
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| 1UGH(E:I) || 1AKZ || 1UGI(A) || Human Uracil-DNA glycosylase || Inhibitor || align="right" | 0.53 || align="right" | 1 || align="right" | 2190
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| 2KAI(AB:I) || 2PKA(XY) || 6PTI || Kallikrein A || Trypsin inhibitor || align="right" | 0.7 || align="right" | 2 || align="right" | 1420
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| 2PTC(E:I) || 2PTN || 6PTI || &beta;-Trypsin || Pancreatic trypsin inhibitor || align="right" | 0.32 || align="right" | 0 || align="right" | 1430
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| 2SIC(E:I) || 1SUP || 3SSI || Subtilisin BPN || Subtilisin inhibitor || align="right" | 0.4 || align="right" | 0 || align="right" | 1620
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| 2SNI(E:I) || 1SUP || 2C12(I) || Subtilisin Novo || Chymotrypsin inhibitor 2 || align="right" | 0.37 || align="right" | 0 || align="right" | 1630
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| colspan="8" | Unbound-bound (6)
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| 1PPE(E:I) || 2PTN || 1PPE(I) || Trypsin || CMT-I || align="right" | 0.27 || align="right" | 0 || align="right" | 1690
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| 1STF(E:I) || 1PPN || 1STF(I) || Papain || Stefin B || align="right" | 0.25 || align="right" | 0 || align="right" | 1790
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| 1TAB(E:I) || 2PTN || 1TAB(I) || Trypsin || BBI || align="right" | 0.27 || align="right" | 0 || align="right" | 1360
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| 1UDI(E:I) || 1UDH || 1UDI(I) || Virus Uracil-DNA glycosylase || Inhibitor || align="right" | 0.36 || align="right" | 0 || align="right" | 2020
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| 2TEC(E:I) || 1THM || 2TEC(I) || Thermitase || Eglin C || align="right" | 0.19 || align="right" | 0 || align="right" | 1560
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| 4HTC(LH:I) || 2HNT(LCEF) || 4HTC(I) || A-Thrombin || Hirudin || align="right" | 0.56 || align="right" | 2 || align="right" | 3320
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| colspan="8" bgcolor="#eeeeee" | '''Antibody-antigen (19)'''
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| colspan="8" | Unbound-unbound (5)
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| 1AHW(DE:F) || 1FGN(LH) || 1BOY || Antibody Fab 5G9 || Tissue factor || align="right" | 0.71 || align="right" | 1 || align="right" | 1900
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| 1BVK(DE:F) || 1BVL(LH) || 3LZT || Antibody Hulysll Fv || Lysozyme || align="right" | 1.22 || align="right" | 3 || align="right" | 1400
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| 1DQJ(AB:C) || 1DQQ(LH) || 3LZT || Hyhel-63 Fab || Lysozyme || align="right" | 0.73 || align="right" | 3 || align="right" | 1760
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| 1MLC(AB:E) || 1MLB(AB) || 1LZA || IgG1 D44.1 Fab fragment || Lysozyme || align="right" | 0.85 || align="right" | 3 || align="right" | 1390
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| 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
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| 1EO8(LH:A) || 1EO8(LH) || 2VIU(A) || Bh151 Fab || Influenza virus hemagglutinin || align="right" | 0.28 || align="right" | 0 || align="right" | 1530
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| 1FBI(LH:X) || 1FBI(LH) || 1HHL || IgG1 Fab fragment || Lysozyme || align="right" | 0.5 || align="right" | 0 || align="right" | 1690
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| 1IAI(MI:LH) || 1AIF(LH) || 1IAI(LH) || IgG1 Idiotypic Fab || Igg2A anti-idiotypic Fab || align="right" | 0.99 || align="right" | 12 || align="right" | 1890
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| 1JHL(LH:A) || 1JHL(LH) || 1GHL(A) || IgG1 Fv fragment || Lysozyme || align="right" | 0.26 || align="right" | 0 || align="right" | 1240
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| 1KXQ(D:E) || 1PIF(A) || 1KXQ(E) || &alpha;-Amylase || Camelid AMD9 Vhh domain || align="right" | 0.43 || align="right" | 0 || align="right" | 2140
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| 1KXT(A:B) || 1PIF(A) || 1KXT(B) || &alpha;-Amylase || Camelid AMB7 Vhh domain || align="right" | 0.39 || align="right" | 0 || align="right" | 1620
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| 1KXV(A:C) || 1PIF(A) || 1KXV(C) || &alpha;-Amylase || Camelid AMD10 Vhh domain || align="right" | 0.24 || align="right" | 0 || align="right" | 1620
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| 1MEL(B:M) || 1MEL(B) || 1LZA || Vh single-domain antibody || Lysozyme || align="right" | 0.65 || align="right" | 2 || align="right" | 1690
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| 1NCA(LH:N) || 1NCA(LH) || 7NN9 || Fab NC41 || Influenza virus neuraminidase || align="right" | 0.24 || align="right" | 0 || align="right" | 1950
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| 1NMB(LH:N) || 1NMB(LH) || 7NN9 || Fab NC10 || Influenza virus neuraminidase || align="right" | 0.21 || align="right" | 0 || align="right" | 1350
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| 1QFU(LH:A) || 1QFU(LH) || 2VIU(A) || Igg1-k Fab || Influenza virus hemagglutinin || align="right" | 0.27 || align="right" | 0 || align="right" | 1840
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| 2JEL(LH:P) || 2JEL(LH) || 1POH || Jel42 Fab fragment || A06 phosphotransferase || align="right" | 0.18 || align="right" | 0 || align="right" | 1500
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| 2VIR(AB:C) || 2VIR(AB) || 2VIU(A) || Igg1-lamda Fab || Influenza virus hemagglutinin || align="right" | 0.41 || align="right" | 1 || align="right" | 1260
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| colspan="8" bgcolor="#eeeeee" | '''Others (11)'''
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| colspan="8" | Unbound-unbound (5)
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| 1AVZ(B:C) || 1AVV || 1SHF(A) || HIV-1 NEF || FYN tyrosin kinase SH3 domain || align="right" | 0.73 || align="right" | 1 || align="right" | 1260
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| 1L0Y(A:B) || 1BEC || 1B1Z(A) || T-cell receptor &beta; chain || Exotoxin A1 || align="right" | 0.83 || align="right" | 2 || align="right" | 1130
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| 1WQ1(G:R) || 1WER || 5P21 || RAS activating domain || RAS || align="right" | 0.83 || align="right" | 9 || align="right" | 2910
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| 2MTA(LH:A) || 2BBK(LH) || 1AAN || Methylamine dehydrogenase || Amicyanin || align="right" | 0.34 || align="right" | 0 || align="right" | 1460
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| 2PCC(A:B) || 1CCA || 1YCC || Cytochrome C peroxidase || Iso-1-Cytochrome C || align="right" | 0.44 || align="right" | 1 || align="right" | 1140
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| colspan="8" | Unbound-bound (6)
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| 1A0O(A:B) || 1CHN || 1A0O(B) || Che A || Che Y || align="right" | 1.59 || align="right" | 9 || align="right" | 1130
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| 1ATN(A:D) || 1ATN(A) || 3DNI || Actin || Deoxyribonuclease I || align="right" | 0.31 || align="right" | 0 || align="right" | 1770
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| 1GLA(G:F) || 1GLA(G) || 1F3G || Glycerol kinase || GSF III || align="right" | 0.37 || align="right" | 0 || align="right" | 1300
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| 1IGC(LH:A) || 1IGC(LH) || 1IGD || IgG1 Fab fragment || Protein G || align="right" | 0.74 || align="right" | 1 || align="right" | 1330
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| 1SPB(S:P) || 1SUP || 1SPB(P) || Subtilisin || Subtilisin prosegment || align="right" | 0.35 || align="right" | 0 || align="right" | 2230
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| 2BTF(A:P) || 2BTF(A) || 1PNE || &beta;-Actin || Profilin || align="right" | 0.29 || align="right" | 0 || align="right" | 2060
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| colspan="8" bgcolor="#eeeeee" | '''Difficult test cases (7)'''
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| colspan="8" | Unbound-unbound (5)
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| 1BTH(LH:P) || 2HNT(LCEF) || 6PTI || Thrombin mutant || Pancreatic trypsin inhibitor || align="right" | 1.91 || align="right" | 18 || align="right" | 2370
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| 1FIN(A:B) || 1HCL || 1VIN || CDK2 cyclindependant kinase 2 || Cyclin || align="right" | 4.66 || align="right" | 59 || align="right" | 3400
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| 1FQ1(B:A) || 1B39(A) || 1FPZ(F) || CDK2 || KAP || align="right" | 3.55 || align="right" | 23 || align="right" | 1830
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| 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
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| 1KKL(AC:H) || 1JB1 || 1SPH(A) || HPr kinase || Phosphocarrier protein Hpr || align="right" | 2.53 || align="right" | 28 || align="right" | 1640
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| colspan="8" | Unbound-bound (2)
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| 1EFU(A:B) || 1D8T(A) || 1EFU(B) || ''E. coli'' Ef-Tu || Efts || align="right" | 2.57 || align="right" | 109 || align="right" | 3630
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| 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.
'''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/>
'''c''' Number of interface C&alpha; atoms with RMSD larger than 2Å between unbound and bound structures after superposition.<br/>
'''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>
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<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>
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== See also ==
* [[Protein-Protein Docking Benchmark|Protein-Protein Docking Benchmark 2.0]]

== References ==
<references/>

[[Category:Academic Research]]