The predictive model developed in PRODIGY was trained using a subset of bound structures from the structure-based protein–protein binding affinity benchmark of Kastritis et al. (2011). It contains 144 non-redundant protein–protein complexes with known 3D structures (of both the unbound and bound components) and associated experimental binding affinity (ΔG) values.
From this dataset we obtained our “reliable” dataset on which we trained our model according to the following cases:
  • Removing cases with not unique values of ΔG
  • Removing the complexes that showed gaps or unresolved fragments at the binding interface (considering a gap to be a missing segment longer than two residues)
  • Removing the complexes for which the ΔG has been measured with a less reliable experimental technique according to the results we reported in Vangone and Bonvin, eLife (2015).
In the following table experimental data, number of ICs and NIS properties have been reported for our 'cleaned' dataset made of 81 protein-protein complexes.
Download the table here (.csv files)
PDB Chains Type ΔG_exp Method i-RMSD BSA ICs_CC ICs_CP ICs_CA ICs_PP ICs_PA ICs_AA NIS_P NIS_A NIS_C ΔG_pred
1A2K.pdb C:AB OG -9.3 ITC 1.11 1603 5 4 20 2 11 25 31.65 41.77 26.58 -9.0
1ACB.pdb E:I EI -13.1 spectroscopy 1.08 1544 3 2 19 4 19 25 42.72 38.5 18.78 -11.9
1AK4.pdb A:D OX -6.4 ITC 1.33 1029 0 4 14 1 10 20 27.95 45.41 26.64 -7.3
1AKJ.pdb AB:DE OX -5.3 SPR 1.14 1995 8 20 7 18 18 2 35.18 35.18 29.64 -7.3
1ATN.pdb A:D OX -12.1 spectroscopy 3.28 1774 9 8 20 4 15 28 36.32 34.94 28.74 -10.9
1AVZ.pdb B:C NC -6.5 ITC 0.73 1259 5 8 9 2 14 10 30.60 42.54 26.87 -8.4
1B6C.pdb A:B OX -8.9 SPR 1.96 1752 6 11 18 1 11 21 31.53 35.35 33.12 -9.4
1BJ1.pdb HL:VW AB -11.6 SPR 0.5 1731 3 8 21 7 22 19 41.70 35.68 22.61 -12.2
1BUH.pdb A:B EI -9.7 SPR 0.75 1324 12 4 20 0 5 17 28.83 41.24 29.93 -8.4
1BVK.pdb DE:F A -10.5 stopped-flow 1.24 1321 2 8 18 2 14 14 43.75 33.59 22.66 -11.3
1BVN.pdb P:T EI -15.1 SPR 0.87 2222 3 12 22 0 23 33 38.22 36.78 25 -13.3
1CBW.pdb ABC:D NC -10.7 spectroscopy 0.74 1457 3 10 26 1 13 28 39.71 39.71 20.59 -11.3
1DE4.pdb AB:CF OX -9.8 SPR 2.59 2066 5 13 17 9 14 9 35.21 33.85 30.94 -8.9
1DQJ.pdb AB:C A -11.7 SPR 0.75 1765 2 20 18 11 25 15 47.79 31.37 20.83 -12.7
1E4K.pdb AB:C OR -7.9 SPR 2.59 1634 3 8 26 2 5 21 38.88 35.97 25.16 -9.4
1E6E.pdb A:B ES -8.3 SPR 1.33 2315 18 15 17 5 11 11 26.09 42.75 31.16 -8.6
1E6J.pdb HL:P A -10.3 SPR 1.05 1245 0 7 8 5 15 26 40.76 38.77 20.48 -9.1
1E96.pdb A:B OG -7.4 ITC 0.71 1179 4 7 16 4 11 8 28.74 37.16 34.1 -8.0
1EER.pdb A:BC OR -15.6 SPR 2.44 3347 30 19 25 12 31 19 26.12 43.75 30.13 -13.6
1EFN.pdb B:A OX -10.1 SPR 0.9 1253 5 5 12 1 12 16 27.48 44.27 28.24 -8.0
1EMV.pdb A:B EI -18.6 stopped-flow 1.28 1535 4 12 11 4 24 13 29.70 29.09 41.21 -11.0
1EWY.pdb A:C ES -7.4 spectroscopy 0.8 1502 9 10 15 3 9 12 29.83 36.95 33.22 -8.3
1EZU.pdb C:AB EI -13.8 spectroscopy 1.21 2751 7 9 33 8 28 42 30.59 40.43 28.99 -13.1
1FC2.pdb C:D OX -10.4 stopped-flow 1.69 1307 4 4 9 8 14 11 37.56 35.61 26.83 -8.5
1FFW.pdb A:B OX -8.1 ITC 1.43 1170 7 2 16 0 2 15 21.85 44.37 33.77 -5.7
1FSK.pdb BC:A AB -13.1 SPR 0.45 1623 7 10 22 3 15 25 40.61 35.81 23.58 -11.7
1GCQ.pdb B:C OX -6.5 SPR 0.92 1208 5 7 11 0 12 21 33.33 41.18 25.49 -9.0
1GLA.pdb G:F ER -6.8 spectroscopy 0.98 1304 5 8 13 0 11 9 26.35 38.82 34.82 -8.1
1GXD.pdb A:C EI -11.7 SPR 1.39 2445 16 6 33 0 15 35 30.31 40 29.69 -12.6
1HE8.pdb B:A OG -7.4 stopped-flow 0.92 1305 8 15 6 5 8 6 33.18 33.33 33.48 -7.3
1I2M.pdb A:B OG -15.8 stopped-flow 2.12 2779 20 17 37 7 26 12 30.41 38.63 30.96 -14.6
1I4D.pdb D:AB OG -7.5 ITC 1.41 1657 3 9 9 7 21 18 31.25 35.1 33.65 -9.3
1J2J.pdb A:B OG -8.1 SPR 0.63 1209 3 4 12 1 3 20 31.79 30.46 37.75 -7.0
1JPS.pdb HL:T A -13.6 SPR 0.51 1852 13 16 18 4 20 12 40.81 34.83 24.36 -12.9
1JTG.pdb B:A EI -12.8 SPR 0.49 2600 11 19 34 4 15 25 32.18 40.83 26.99 -11.6
1JWH.pdb CD:A ER -11.1 ITC 1.27 1451 2 5 20 0 10 20 33.27 34.18 32.55 -9.5
1K5D.pdb AB:C OG -12.8 stopped-flow 1.19 2527 16 15 24 6 21 27 25.89 33.61 40.5 -11.6
1KAC.pdb A:B OR -10.7 SPR 0.95 1456 7 5 13 2 18 12 42.86 37.66 19.48 -11.9
1KKL.pdb ABC:H ES -10 SPR 2.2 1641 6 9 16 4 14 22 31.19 38.1 30.71 -9.1
1KTZ.pdb A:B OR -8.9 SPR 0.39 989 5 6 7 0 5 12 38.18 33.94 27.88 -8.1
1KXQ.pdb H:A AB -11.5 SPR 0.72 2172 7 9 18 12 25 23 40.46 34.54 25 -11.8
1LFD.pdb B:A OG -7.8 stopped-flow 1.79 1167 9 8 9 3 9 11 32.46 29.32 38.22 -8.4
1M10.pdb A:B ER -11.2 SPR 2.1 2097 16 24 24 2 8 12 35.08 36.31 28.62 -10.5
1MLC.pdb AB:E NC -9.6 SPR 0.6 1392 5 8 15 13 18 8 45.63 33.01 21.36 -10.3
1MQ8.pdb A:B OX -7.5 SPR 1.76 1241 3 11 10 6 15 11 31.79 37.14 31.07 -8.2
1P2C.pdb AB:C A -13.6 SPR 0.46 1456 5 8 17 13 22 10 45.06 32.66 22.28 -11.4
1PPE.pdb E:I EI -15.6 spectroscopy 0.34 1688 5 10 28 0 20 24 47.09 34.88 18.02 -14.7
1PVH.pdb A:B OR -9.5 ITC 0.34 1403 5 8 8 4 21 11 38.13 35.12 26.76 -10.9
1QA9.pdb A:B OX -7.2 SPR 0.73 1353 21 10 14 0 2 3 35.22 25.79 38.99 -9.6
1R0R.pdb E:I EI -14.2 spectroscopy 0.45 1409 1 13 8 6 21 31 46.67 37.14 16.19 -11.3
1S1Q.pdb A:B OX -4.3 SPR 0.98 1288 1 4 11 6 16 16 35.67 35.67 28.65 -9.0
1US7.pdb A:B ER -8.1 ITC 1.06 1106 6 6 10 1 5 14 27.60 33.77 38.64 -6.8
1VFB.pdb AB:C A -11.5 ITC 1.02 1383 2 8 20 3 13 14 45.67 31.89 22.44 -11.4
1WEJ.pdb HL:F A -12.5 spectroscopy 0.31 1177 10 9 18 2 4 8 41.26 34.47 24.27 -9.4
1XQS.pdb A:C OX -7.1 SPR 1.77 2350 24 18 24 7 15 3 29.74 35.29 34.97 -11.2
1XU1.pdb ABD:T OR -11.2 SPR 1.3 1700 8 12 21 3 10 16 31.76 39.19 29.05 -9.1
1Z0K.pdb A:B OG -7 SPR 0.53 1787 5 7 14 2 21 27 34.78 30.43 34.78 -11.7
1ZHI.pdb A:B OX -9.1 ITC 0.68 1322 5 4 18 2 12 12 28.03 38.26 33.71 -8.7
2A9K.pdb A:B ES -10.2 ITC 0.85 1751 4 15 23 6 23 14 30.08 31.95 37.97 -11.5
2ABZ.pdb B:E EI -11.7 spectroscopy 0.9 1447 4 2 18 4 18 25 44.02 34.62 21.37 -12.0
2AJF.pdb A:E OR -10.6 SPR 0.65 1704 1 8 18 5 19 10 37.72 35.96 26.32 -10.8
2AQ3.pdb A:B NC -6.7 ITC 1.82 1105 2 7 7 6 7 15 39.44 30.68 29.88 -7.4
2C0L.pdb A:B OX -9.8 ITC 2.62 2013 9 9 13 3 25 28 27.78 40.28 31.94 -11.2
2FJU.pdb B:A OG -7.2 SPR 1.04 1245 3 4 6 3 6 18 28.97 39.28 31.75 -5.9
2GOX.pdb A:B OX -12.1 SPR 0.6 1631 13 6 17 3 19 6 30.47 35.62 33.91 -11.3
2HQS.pdb A:H OX -10.2 ITC 1.14 2333 10 21 37 5 17 19 33.24 43.88 22.87 -12.1
2HRK.pdb A:B OX -11 SPR 2.03 1595 8 11 14 1 9 13 32.47 40.26 27.27 -8.7
2I25.pdb N:L A -12.3 SPR 1.21 1425 7 7 17 2 18 13 39.11 31.84 29.05 -12.0
2MTA.pdb HL:A ES -7.4 spectroscopy 0.41 1461 3 3 21 2 11 24 24.53 45.75 29.72 -7.8
2NYZ.pdb AB:D OR -12.7 SPR 2.09 2160 6 10 18 5 25 20 38.50 36.41 25.09 -12.7
2OOB.pdb A:B ES -5.7 ITC 0.85 808 3 3 13 0 2 15 27.17 34.78 38.04 -6.2
2PCB.pdb A:B NC -6.8 ITC 0.45 1029 11 4 7 3 7 1 30.87 35.37 33.76 -7.4
2PCC.pdb A:B ES -7.9 ITC 0.39 1141 8 6 5 2 10 8 32.81 34.7 32.49 -8.1
2TGP.pdb Z:I NC -7.5 spectroscopy 0.57 1432 4 9 28 1 14 20 43.00 38.65 18.36 -12.3
2VIR.pdb AB:C A -12.3 SPR 0.8 1263 0 5 8 9 25 12 43.16 38.02 18.82 -10.9
2VIS.pdb AB:C NC -7.4 SPR 0.8 1296 0 5 8 7 23 16 43.68 37.93 18.39 -11.0
2WPT.pdb A:B NC -10.7 stopped-flow 1.61 1581 8 14 12 2 28 10 23.13 27.21 49.66 -11.9
3BZD.pdb A:B OX -9.6 ITC 1.08 1312 4 7 6 7 15 12 41.04 29.48 29.48 -9.4
3CPH.pdb G:A OG -8.8 ITC 2.12 1685 6 7 14 2 15 19 28.77 35.73 35.5 -9.3
3SGB.pdb E:I EI -14.5 spectroscopy 0.36 1268 3 5 15 2 20 20 49.42 36.05 14.53 -13.1
4CPA.pdb A:I EI -11.3 spectroscopy 1.52 1177 0 3 16 5 10 19 47.96 31.67 20.36 -10.1
Table information:
(a) PDB= PDB entry; Chains=Interacting chains (AB:C to represent a complex where chains A and B make up component 1, chain C, component 2); Type=Functional class of the complex; ΔG_exp= Experimental measured ΔG Method=Experimental technique used to measure the ΔG i_RMDS=root-mean-square displacement of the C-alpha atoms of interface residues of the two partners after the unbound and the bound interfaces have been superimposed by least-square; BSABuried Surface Area upon complex formation; ICs_XX=Number of ICs divided by their charged(C)/polar(P)/apolar(A) character; NIS_X=Percentage of the charged(C), polar(P) and apolar(A) NIS (Non-Interacting Surface) residues; ΔG_pred=Values of ΔG predicted by PRODIGY.
(b) Functional classes: A antigen/antibody; AB antigen/antibody with bound antibody; EI enzyme/inhibitor; ES enzyme/substrate; ER enzyme complex with a regulatory or accessory chain ; OG G-protein containing ; OR receptor containing ; OX miscellaneous ; NC non-cognate.
(c)Experimental methods: ITC Isotermal Titration Calorimetry; SPR Surface Plasmon Resonance.
For further information please refer to Vangone and Bonvin, eLife (2015).
Download the dataset at this link (.pdb files compressed in a .tgz file)
Please note that the provided PDB files have been 'cleaned' according to the folllwing points:
  • All the HETATM entries have been removed from the .pdb file
  • The chains have been renamed as A for the receptor (i.e. the biggest protein in the complex) and B for the ligand. In the case of multiple chains for either the receptor and/or the ligand in the original file, a shift of +500 for each chain has been applied to the numbering to avoid overlap in the residues numbering.
  • Residue with double occupancy were removed
  • The hydrogens have been removed
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