Christoph at 05:08, 19 October 2008

2008-10-19T05:08:31Z

Christoph at 02:30, 30 September 2006

2006-09-30T02:30:26Z

Christoph at 02:21, 30 September 2006

2006-09-30T02:21:21Z

New page

<div style="float:left; margin:0px 20px 20px 0px;">
{| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
|-
! colspan="8" bgcolor="#EFEFEF" | '''Benchmarks'''
|-align="center" style="background-color:#1188ee; color:#ffffff;"
!Complex<sup>a</sup>
!Receptor<sup>a</sup>
!Ligand<sup>a</sup>
!Receptor description
!Ligand description
!RMSD<sup>b</sup>(Å)
!Cα<sup>c</sup>
!ΔASA<sup>d</sup>(Å<sup>2</sup>)
|-
| colspan="8" bgcolor="#eeeeee" | '''Enzyme-inhibitor (22)'''
|-
| colspan="8" | Unbound-unbound (16)
|-
| {{rcsb|1ACB|1ACB(E:I)}} || 5CHA(A) || 1CSE(I) || α-Chymotrypsin || Eglin C || align="right" | 0.7 || align="right" | 1 || align="right" | 1540
|-
| 1AVW(A:B) || 2PTN || 1BA7(A) || Trypsin || Soybean trypsin inhibitor || align="right" | 0.35 || align="right" | 0 || align="right" | 1740
|-
| 1BRC(E:I) || 1BRA || 1AAP(A) || Trypsin || APPI || align="right" | 0.44 || align="right" | 0 || align="right" | 1320
|-
| 1BRS(A:D) || 1A2P(B) || 1A19(A) || Barnase || Barstar || align="right" | 0.47 || align="right" | 0 || align="right" | 1560
|-
| 1CGI(E:I) || 1CHG || 1HPT || α-Chymotrypsinogen || Pancreatic secretory trypsin inhibitor || align="right" | 1.48 || align="right" | 14 || align="right" | 2050
|-
| 1CHO(E:I) || 5CHA(A) || 2OVO || α-Chymotrypsin || Ovomucoid 3rd domain || align="right" | 0.59 || align="right" | 1 || align="right" | 1470
|-
| 1CSE(E:I) || 1SCD || 1ACB(I) || Subtilisin Carlsberg || Eglin C || align="right" | 0.43 || align="right" | 0 || align="right" | 1490
|-
| 1DFJ(I:E) || 2BNH || 7RSA || Ribonuclease inhibitor || Ribonuclease A || align="right" | 1.04 || align="right" | 13 || align="right" | 2580
|-
| IFSS(A:B) || 2ACE(E) || 1FSC || Snake venom acetylcholinesterase || Fasciculin II || align="right" | 0.75 || align="right" | 1 || align="right" | 1970
|-
| 1MAH(A:F) || 1MAA(B) || 1FSC || Mouse acetylcholinesterase || Fasciculin II || align="right" | 0.6 || align="right" | 0 || align="right" | 2150
|-
| 1TGS(Z:I) || 2PTN || 1HPT || Trypsinogen || Pancreatic secretory trypsin inhibitor || align="right" | 1.49 || align="right" | 17 || align="right" | 1720
|-
| 1UGH(E:I) || 1AKZ || 1UGI(A) || Human Uracil-DNA glycosylase || Inhibitor || align="right" | 0.53 || align="right" | 1 || align="right" | 2190
|-
| 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 || β-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) || α-Amylase || Camelid AMD9 Vhh domain || align="right" | 0.43 || align="right" | 0 || align="right" | 2140
|-
| 1KXT(A:B) || 1PIF(A) || 1KXT(B) || α-Amylase || Camelid AMB7 Vhh domain || align="right" | 0.39 || align="right" | 0 || align="right" | 1620
|-
| 1KXV(A:C) || 1PIF(A) || 1KXV(C) || α-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 β 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 || β-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-α, Gi-α chimera || Gt-β-γ || 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.
'''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.<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 Cα atoms with RMSD larger than 2Å between unbound and bound structures after superposition.<br/>
'''d''' ΔASA: 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>
|}
<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>

== See also ==
* [[Protein-Protein Docking Benchmark|Protein-Protein Docking Benchmark 2.0]]

== References ==
<references/>

[[Category:Academic Research]]

@@ Line 160: / Line 160: @@
 <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>
+<br clear="all"/>
 == See also ==
 * [[Protein-Protein Docking Benchmark|Protein-Protein Docking Benchmark 2.0]]

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 {| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
 |-
-! colspan="8" bgcolor="#EFEFEF" | '''Benchmarks'''
+! colspan="8" bgcolor="#EFEFEF" | '''Protein-Protein Docking Benchmark 1.0'''
 |-align="center" style="background-color:#1188ee; color:#ffffff;"
 !Complex<sup>a</sup>

Protein-Protein Docking Benchmark 1.0 - Revision history

Christoph at 05:08, 19 October 2008

Christoph at 02:30, 30 September 2006

Christoph at 02:21, 30 September 2006