Build Database Docking Decoys Info
 
   
 
Construction of docking decoys:

Sets of possible protein-protein solutions, including at least one near-native solution, are important for testing protein-protein docking scoring functions. The protein-protein docking decoys are built by Gramm-X without the refinement stage. The L-RMSD (RMSD of the backbone atoms of the ligand), I-RMSD (RMSD of the backbone atoms of the interface residues), fnat( number of native(correct) residue-residue contacts in the predicted complex divided by the number of contacts in the native complex) and fnon-nat(number of non-native (incorrect) residue-residue contacts in the predicted complex divided by the total number of contacts in the complex) of 500,000 matches from scan stage are computed according to the CAPRI evaluation protocol (Raul Mendez et al, Proteins, 2005). A solution with L-RMSD < 5.0 Å is defined as near-native one. The sets contain top 100 nonnear-native structures with the highest surface complementarity scores. The unbound structures are from DOCKGROUND benchmark set Version 2.
 
Protein-protein docking decoys:

Download protein-protein docking decoys in a zipped archive [size: 520M]
         
Separately, each decoys set is available in the following table.
Protein-Protein Docking Decoys Set 1.0          
Download a Complex b Class.Help information. Need Javascript enabled Rec. c Chain d RMSD e Res. f Lig. c Chain d RMSDe Res.f RMSD g Hitsh
decoy 1a2k_AB_C 0 1gy6 AB:AB 1.32 1.60 3ran A:C 1.33 2.15 4.35 2
decoy 1akj_AB_DE 0 1i4f AB:AB 3.18 1.40 1cd8 A1A2:DE 0.99 2.60 4.06 10
decoy 1bui_A_C 0 1ddj A:A 1.85 2.00 2sak A:C 1.67 1.80 2.39 10
decoy 1e96_A_B 0 1mh1 A:A 0.73 1.38 1hh8 A:B 0.62 1.80 2.82 10
decoy 1ewy_A_C 0 2bmw A:A 1.01 1.50 1czp A:C 0.89 1.17 3.92 10
decoy 1f51_AB_E 0 1ixm AB:AB 2.27 2.60 1nat A:E 0.74 2.45 4.14 10
decoy 1f6m_A_C 0 1trb A:A 7.29 2.00 2trx A:C 1.00 1.68 3.63 10
decoy 1g20_AB_EF 0 1l5h AB:AB 1.73 2.30 1fp6 AB:EF 2.69 2.15 3.62 10
decoy 1gpw_A_B 0 1thf D:A 3.56 1.45 1k9v F:B 0.69 2.40 2.59 10
decoy 1he1_A_C 0 1he9 A:A 0.91 2.40 1mh1 A:C 0.75 1.38 1.73 10
decoy 1he8_A_B 0 1e8y A:A 2.31 2.00 2evw X:B 1.20 1.05 4.93 1
decoy 1hxy_AB_D 0 1t5w AB:AB 2.27 2.40 1enf A:D 0.52 1.69 4.24 2
decoy 1l9b_LMH_C 0 1rzh LMH:LMH 1.77 1.80 1cxc A:C 0.89 1.60 3.97 10
decoy 1ma9_A_B 0 1kw2 A:A 0.99 2.15 2fxu A:B 9.53 1.35 2.86 10
decoy 1nbf_A_D 0 1nb8 A:A 3.83 2.30 1yj1 A:D 1.73 1.30 3.85 10
decoy 1ook_AB_G 0 2cf8 LH:AB 1.54 1.30 1p9a G:G 0.69 1.70 3.13 3
decoy 1p7q_AB_D 0 1i4f AB:AB 1.30 1.40 1ugn A:D 1.90 1.80 3.36 4
decoy 1r4m_AB_I 0 1yov AB:AB 3.90 2.60 1ndd A:I 1.34 1.60 3.93 1
decoy 1s6v_A_B 0 2eut A:A 0.96 1.12 1ycc A:B 1.97 1.23 3.18 4
decoy 1uex_AB_C 0 1jwi AB:AB 0.40 2.00 1ijb A:C 0.68 1.80 4.90 1
decoy 1w1i_A_F 0 2bub A:A 0.93 2.66 1vfl A:F 0.28 1.80 2.20 4
decoy 1wq1_R_G 0 2evw X:R 1.15 1.05 1wer A:G 0.83 1.60 3.23 10
decoy 1xd3_A_B 0 1uch A:A 2.45 1.80 1yj1 A:B 2.73 1.30 3.64 10
decoy 1yvb_A_I 0 2ghu A:A 0.54 3.10 1cew I:I 0.84 2.00 2.94 10
decoy 1zy8_AB_K 0 1zmd AB:A1B1 0.54 2.08 2f60 K:K1 0.90 1.55 1.14 10
decoy 1zy8_AB_K 0 1zmd AB:A2B2 0.84 2.08 2f60 K:K2 0.67 1.55 1.68 9
decoy 2a5t_A_B 0 1pb7 A:A 2.73 1.35 2a5s A:B 2.31 1.70 4.95 1
decoy 2ckh_A_B 0 2ckg A:A 0.82 2.45 1wm3 A:B 0.76 1.20 2.47 10
decoy 2goo_A_C 0 1reu A:A 1.08 2.65 1bte A:C 1.40 1.50 3.90 10
decoy 3fap_A_B 0 1bkf A:A 0.63 1.60 1aue A:B 0.69 2.33 3.67 10
decoy 3pro_A_C 0 1ssx A:A 2.94 0.83 2pro A:C 1.86 3.00 2.82 10
decoy 1avw_A_B 1 2a31 A:A 0.78 1.25 1avu A:B 0.76 2.30 2.92 10
decoy 1bth_LH_P 1 2cf8 LH:LH 4.89 1.30 1bpi A:P 1.48 1.09 3.93 1
decoy 1bvn_P_T 1 1hx0 A:P 0.63 1.38 1ok0 A:T 0.42 0.93 2.24 10
decoy 1cho_E_I 1 1k2i 1:E 0.42 1.80 2ovo A:I 1.11 1.50 2.73 10
decoy 1dfj_E_I 1 1dy5 A:E 0.83 0.87 2bnh 0:I 1.53 2.30 3.54 9
decoy 1ezu_AB_C 1 1ecz AB:AB 2.27 2.68 1dpo A:C 0.79 1.59 2.39 10
decoy 1gpq_A_D 1 1xs0 A:A 1.34 1.58 3lzt A:D 0.87 0.93 2.32 10
decoy 1ku6_A_B 1 2c0q A:A 4.06 2.50 1fas A:B 0.71 1.80 4.37 10
decoy 1oph_A_B 1 1qlp A:A 3.12 2.00 1hj9 A:B 2.53 0.95 1.28 10
decoy 1ppf_E_I 1 1b0f A:E 2.18 3.00 2ovo A:I 2.03 1.50 2.99 10
decoy 1t6g_A_C 1 1t6e X:A 0.40 1.70 1bk1 A:C 1.06 2.00 3.78 10
decoy 1tmq_A_B 1 1jae A:A 0.77 1.65 1b1u A:B 1.42 2.20 2.07 10
decoy 1tx6_A_I 1 2a31 A:A 1.60 1.25 1c2a A:I 1.73 1.90 2.75 10
decoy 1ugh_E_I 1 1akz A:E 0.61 1.57 1ugi A:I 2.60 1.55 2.86 10
decoy 1xx9_A_CD 1 1zhr A:A 1.10 1.73 1ecz AB:CD 10.3 2.68 4.45 2
decoy 2bkr_A_B 1 2bkq A:A 2.33 2.00 1ndd A:B 1.02 1.60 1.58 10
decoy 2fi4_E_I 1 1hj9 A:E 0.70 0.95 1bpi A:I 1.88 1.09 2.61 10
decoy 2kai_AB_I 1 2pka AB:AB 1.90 2.05 1bpi A:I 0.72 1.09 2.87 10
decoy 2sni_E_I 1 1sup A:E 0.26 1.60 2ci2 I:I 0.48 2.00 2.14 10
decoy 3sic_E_I 1 1sup A:E 0.34 1.60 3ssi A:I 0.78 2.30 3.54 10
decoy 1a2y_AB_C 2 1vfa AB:AB 0.69 1.80 3lzt A:C 1.30 0.93 3.70 10
decoy 1g6v_A_K 2 1lug A:A 0.77 0.95 1f2x K:K 0.44 2.10 4.08 6
decoy 1jps_LH_T 2 1jpt LH:LH 1.02 1.85 1boy A:T 1.33 2.20 2.30 10
decoy 1wej_LH_F 2 1qbl LH:LH 0.99 2.26 2b4z A:F 0.99 1.50 1.88 10
decoy 2bnq_AB_DE 2 1i4f AB:AB 1.15 1.40 2bnu AB:DE 1.13 1.40 4.91 1
decoy 1fm9_A_D 0 1mvc A:A 1.30 1.90 1zgy A:D 2.09 1.80 2.03 10
decoy 1r0r_E_I 1 1scn E:E 0.75 1.90 2gkr I:I 1.14 1.16 0.86 10
decoy 1u7f_A_B 0 1mjs A:A 2.26 1.91 1ygs A:B 1.29 2.10 1.19 10
decoy 2btf_A_P 0 2hf4 A:A 1.66 1.80 1pne A:P 1.07 2.00 2.73 10
decoy 1bui_B_C 0 1ddj A:B 2.45 2.00 2sak A:C 1.67 1.80 2.74 10
     
a tar xvzf xxxx_yy_zz.tgz(For example: tar xvzf 1a2k_AB_C.tgz); You will get a file named "rmsd.list" and a directory named "decoys".The format of rmsd.list and the directory are described in README
b xxxx_yy_zz, xxxx:pdb code of co-crystallized structure; yy and zz are interacting chains of co-crystallized structure.
c Rec.: pdb code of unbound structure of protein 1; Lig.: pdb code of unbound structure of protein 2.
d Chains before colon are in unbound structure; chains after colon are in co-crystallized structure.
e C_alpha rmsd of unbound and co-crystallized structure.(Å)
f Crystal structure resolution.(Å)
g The ligand RMSD of the best near-native solution.(Å)
h The number of near-native solution kept in each decoy set.