Dataset
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.
- 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.
| PDB | Chains | Type | ΔG_exp | ΔG_pred | Method | i-RMSD | BSA | ICs_CC | ICs_CP | ICs_CA | ICs_PP | ICs_PA | ICs_AA | NIS_P | NIS_A | NIS_C |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1A2K.pdb | C:AB | OG | -9.3 | -9.0 | ITC | 1.1 | 1603 | 5 | 4 | 20 | 2 | 11 | 25 | 31.6 | 41.8 | 26.6 |
| 1ACB.pdb | E:I | EI | -13.1 | -11.9 | spectroscopy | 1.1 | 1544 | 3 | 2 | 19 | 4 | 19 | 25 | 42.7 | 38.5 | 18.8 |
| 1AK4.pdb | A:D | OX | -6.4 | -7.3 | ITC | 1.3 | 1029 | 0 | 4 | 14 | 1 | 10 | 20 | 27.9 | 45.4 | 26.6 |
| 1AKJ.pdb | AB:DE | OX | -5.3 | -7.3 | SPR | 1.1 | 1995 | 8 | 20 | 7 | 18 | 18 | 2 | 35.2 | 35.2 | 29.6 |
| 1ATN.pdb | A:D | OX | -12.1 | -10.9 | spectroscopy | 3.3 | 1774 | 9 | 8 | 20 | 4 | 15 | 28 | 36.3 | 34.9 | 28.7 |
| 1AVZ.pdb | B:C | NC | -6.5 | -8.4 | ITC | 0.7 | 1259 | 5 | 8 | 9 | 2 | 14 | 10 | 30.6 | 42.5 | 26.9 |
| 1B6C.pdb | A:B | OX | -8.9 | -9.4 | SPR | 2.0 | 1752 | 6 | 11 | 18 | 1 | 11 | 21 | 31.5 | 35.4 | 33.1 |
| 1BJ1.pdb | HL:VW | AB | -11.6 | -12.2 | SPR | 0.5 | 1731 | 3 | 8 | 21 | 7 | 22 | 19 | 41.7 | 35.7 | 22.6 |
| 1BUH.pdb | A:B | EI | -9.7 | -8.4 | SPR | 0.8 | 1324 | 12 | 4 | 20 | 0 | 5 | 17 | 28.8 | 41.2 | 29.9 |
| 1BVK.pdb | DE:F | A | -10.5 | -11.3 | stopped-flow | 1.2 | 1321 | 2 | 8 | 18 | 2 | 14 | 14 | 43.8 | 33.6 | 22.7 |
| 1BVN.pdb | P:T | EI | -15.1 | -13.3 | SPR | 0.9 | 2222 | 3 | 12 | 22 | 0 | 23 | 33 | 38.2 | 36.8 | 25 |
| 1CBW.pdb | ABC:D | NC | -10.7 | -11.3 | spectroscopy | 0.7 | 1457 | 3 | 10 | 26 | 1 | 13 | 28 | 39.7 | 39.7 | 20.6 |
| 1DE4.pdb | AB:CF | OX | -9.8 | -8.9 | SPR | 2.6 | 2066 | 5 | 13 | 17 | 9 | 14 | 9 | 35.2 | 33.9 | 30.9 |
| 1DQJ.pdb | AB:C | A | -11.7 | -12.7 | SPR | 0.8 | 1765 | 2 | 20 | 18 | 11 | 25 | 15 | 47.8 | 31.4 | 20.8 |
| 1E4K.pdb | AB:C | OR | -7.9 | -9.4 | SPR | 2.6 | 1634 | 3 | 8 | 26 | 2 | 5 | 21 | 38.9 | 36.0 | 25.2 |
| 1E6E.pdb | A:B | ES | -8.3 | -8.6 | SPR | 1.3 | 2315 | 18 | 15 | 17 | 5 | 11 | 11 | 26.1 | 42.8 | 31.2 |
| 1E6J.pdb | HL:P | A | -10.3 | -9.1 | SPR | 1.1 | 1245 | 0 | 7 | 8 | 5 | 15 | 26 | 40.8 | 38.8 | 20.5 |
| 1E96.pdb | A:B | OG | -7.4 | -8.0 | ITC | 0.7 | 1179 | 4 | 7 | 16 | 4 | 11 | 8 | 28.7 | 37.2 | 34.1 |
| 1EER.pdb | A:BC | OR | -15.6 | -13.6 | SPR | 2.4 | 3347 | 30 | 19 | 25 | 12 | 31 | 19 | 26.1 | 43.8 | 30.1 |
| 1EFN.pdb | B:A | OX | -10.1 | -8.0 | SPR | 0.9 | 1253 | 5 | 5 | 12 | 1 | 12 | 16 | 27.5 | 44.3 | 28.2 |
| 1EMV.pdb | A:B | EI | -18.6 | -11.0 | stopped-flow | 1.3 | 1535 | 4 | 12 | 11 | 4 | 24 | 13 | 29.7 | 29.1 | 41.2 |
| 1EWY.pdb | A:C | ES | -7.4 | -8.3 | spectroscopy | 0.8 | 1502 | 9 | 10 | 15 | 3 | 9 | 12 | 29.8 | 37.0 | 33.2 |
| 1EZU.pdb | C:AB | EI | -13.8 | -13.1 | spectroscopy | 1.2 | 2751 | 7 | 9 | 33 | 8 | 28 | 42 | 30.6 | 40.4 | 29.0 |
| 1FC2.pdb | C:D | OX | -10.4 | -8.5 | stopped-flow | 1.7 | 1307 | 4 | 4 | 9 | 8 | 14 | 11 | 37.6 | 35.6 | 26.8 |
| 1FFW.pdb | A:B | OX | -8.1 | -5.7 | ITC | 1.4 | 1170 | 7 | 2 | 16 | 0 | 2 | 15 | 21.9 | 44.4 | 33.8 |
| 1FSK.pdb | BC:A | AB | -13.1 | -11.7 | SPR | 0.5 | 1623 | 7 | 10 | 22 | 3 | 15 | 25 | 40.6 | 35.8 | 23.6 |
| 1GCQ.pdb | B:C | OX | -6.5 | -9.0 | SPR | 0.9 | 1208 | 5 | 7 | 11 | 0 | 12 | 21 | 33.3 | 41.2 | 25.5 |
| 1GLA.pdb | G:F | ER | -6.8 | -8.1 | spectroscopy | 1.0 | 1304 | 5 | 8 | 13 | 0 | 11 | 9 | 26.4 | 38.8 | 34.8 |
| 1GXD.pdb | A:C | EI | -11.7 | -12.6 | SPR | 1.4 | 2445 | 16 | 6 | 33 | 0 | 15 | 35 | 30.3 | 40 | 29.7 |
| 1HE8.pdb | B:A | OG | -7.4 | -7.3 | stopped-flow | 0.9 | 1305 | 8 | 15 | 6 | 5 | 8 | 6 | 33.2 | 33.3 | 33.5 |
| 1I2M.pdb | A:B | OG | -15.8 | -14.6 | stopped-flow | 2.1 | 2779 | 20 | 17 | 37 | 7 | 26 | 12 | 30.4 | 38.6 | 31.0 |
| 1I4D.pdb | D:AB | OG | -7.5 | -9.3 | ITC | 1.4 | 1657 | 3 | 9 | 9 | 7 | 21 | 18 | 31.2 | 35.1 | 33.6 |
| 1J2J.pdb | A:B | OG | -8.1 | -7.0 | SPR | 0.6 | 1209 | 3 | 4 | 12 | 1 | 3 | 20 | 31.8 | 30.5 | 37.8 |
| 1JPS.pdb | HL:T | A | -13.6 | -12.9 | SPR | 0.5 | 1852 | 13 | 16 | 18 | 4 | 20 | 12 | 40.8 | 34.8 | 24.4 |
| 1JTG.pdb | B:A | EI | -12.8 | -11.6 | SPR | 0.5 | 2600 | 11 | 19 | 34 | 4 | 15 | 25 | 32.2 | 40.8 | 27.0 |
| 1JWH.pdb | CD:A | ER | -11.1 | -9.5 | ITC | 1.3 | 1451 | 2 | 5 | 20 | 0 | 10 | 20 | 33.3 | 34.2 | 32.5 |
| 1K5D.pdb | AB:C | OG | -12.8 | -11.6 | stopped-flow | 1.2 | 2527 | 16 | 15 | 24 | 6 | 21 | 27 | 25.9 | 33.6 | 40.5 |
| 1KAC.pdb | A:B | OR | -10.7 | -11.9 | SPR | 0.9 | 1456 | 7 | 5 | 13 | 2 | 18 | 12 | 42.9 | 37.7 | 19.5 |
| 1KKL.pdb | ABC:H | ES | -10 | -9.1 | SPR | 2.2 | 1641 | 6 | 9 | 16 | 4 | 14 | 22 | 31.2 | 38.1 | 30.7 |
| 1KTZ.pdb | A:B | OR | -8.9 | -8.1 | SPR | 0.4 | 989 | 5 | 6 | 7 | 0 | 5 | 12 | 38.2 | 33.9 | 27.9 |
| 1KXQ.pdb | H:A | AB | -11.5 | -11.8 | SPR | 0.7 | 2172 | 7 | 9 | 18 | 12 | 25 | 23 | 40.5 | 34.5 | 25 |
| 1LFD.pdb | B:A | OG | -7.8 | -8.4 | stopped-flow | 1.8 | 1167 | 9 | 8 | 9 | 3 | 9 | 11 | 32.5 | 29.3 | 38.2 |
| 1M10.pdb | A:B | ER | -11.2 | -10.5 | SPR | 2.1 | 2097 | 16 | 24 | 24 | 2 | 8 | 12 | 35.1 | 36.3 | 28.6 |
| 1MLC.pdb | AB:E | NC | -9.6 | -10.3 | SPR | 0.6 | 1392 | 5 | 8 | 15 | 13 | 18 | 8 | 45.6 | 33.0 | 21.4 |
| 1MQ8.pdb | A:B | OX | -7.5 | -8.2 | SPR | 1.8 | 1241 | 3 | 11 | 10 | 6 | 15 | 11 | 31.8 | 37.1 | 31.1 |
| 1P2C.pdb | AB:C | A | -13.6 | -11.4 | SPR | 0.5 | 1456 | 5 | 8 | 17 | 13 | 22 | 10 | 45.1 | 32.7 | 22.3 |
| 1PPE.pdb | E:I | EI | -15.6 | -14.7 | spectroscopy | 0.3 | 1688 | 5 | 10 | 28 | 0 | 20 | 24 | 47.1 | 34.9 | 18.0 |
| 1PVH.pdb | A:B | OR | -9.5 | -10.9 | ITC | 0.3 | 1403 | 5 | 8 | 8 | 4 | 21 | 11 | 38.1 | 35.1 | 26.8 |
| 1QA9.pdb | A:B | OX | -7.2 | -9.6 | SPR | 0.7 | 1353 | 21 | 10 | 14 | 0 | 2 | 3 | 35.2 | 25.8 | 39.0 |
| 1R0R.pdb | E:I | EI | -14.2 | -11.3 | spectroscopy | 0.5 | 1409 | 1 | 13 | 8 | 6 | 21 | 31 | 46.7 | 37.1 | 16.2 |
| 1S1Q.pdb | A:B | OX | -4.3 | -9.0 | SPR | 1.0 | 1288 | 1 | 4 | 11 | 6 | 16 | 16 | 35.7 | 35.7 | 28.6 |
| 1US7.pdb | A:B | ER | -8.1 | -6.8 | ITC | 1.1 | 1106 | 6 | 6 | 10 | 1 | 5 | 14 | 27.6 | 33.8 | 38.6 |
| 1VFB.pdb | AB:C | A | -11.5 | -11.4 | ITC | 1.0 | 1383 | 2 | 8 | 20 | 3 | 13 | 14 | 45.7 | 31.9 | 22.4 |
| 1WEJ.pdb | HL:F | A | -12.5 | -9.4 | spectroscopy | 0.3 | 1177 | 10 | 9 | 18 | 2 | 4 | 8 | 41.3 | 34.5 | 24.3 |
| 1XQS.pdb | A:C | OX | -7.1 | -11.2 | SPR | 1.8 | 2350 | 24 | 18 | 24 | 7 | 15 | 3 | 29.7 | 35.3 | 35.0 |
| 1XU1.pdb | ABD:T | OR | -11.2 | -9.1 | SPR | 1.3 | 1700 | 8 | 12 | 21 | 3 | 10 | 16 | 31.8 | 39.2 | 29.1 |
| 1Z0K.pdb | A:B | OG | -7 | -11.7 | SPR | 0.5 | 1787 | 5 | 7 | 14 | 2 | 21 | 27 | 34.8 | 30.4 | 34.8 |
| 1ZHI.pdb | A:B | OX | -9.1 | -8.7 | ITC | 0.7 | 1322 | 5 | 4 | 18 | 2 | 12 | 12 | 28.0 | 38.3 | 33.7 |
| 2A9K.pdb | A:B | ES | -10.2 | -11.5 | ITC | 0.8 | 1751 | 4 | 15 | 23 | 6 | 23 | 14 | 30.1 | 31.9 | 38.0 |
| 2ABZ.pdb | B:E | EI | -11.7 | -12.0 | spectroscopy | 0.9 | 1447 | 4 | 2 | 18 | 4 | 18 | 25 | 44.0 | 34.6 | 21.4 |
| 2AJF.pdb | A:E | OR | -10.6 | -10.8 | SPR | 0.7 | 1704 | 1 | 8 | 18 | 5 | 19 | 10 | 37.7 | 36.0 | 26.3 |
| 2AQ3.pdb | A:B | NC | -6.7 | -7.4 | ITC | 1.8 | 1105 | 2 | 7 | 7 | 6 | 7 | 15 | 39.4 | 30.7 | 29.9 |
| 2C0L.pdb | A:B | OX | -9.8 | -11.2 | ITC | 2.6 | 2013 | 9 | 9 | 13 | 3 | 25 | 28 | 27.8 | 40.3 | 31.9 |
| 2FJU.pdb | B:A | OG | -7.2 | -5.9 | SPR | 1.0 | 1245 | 3 | 4 | 6 | 3 | 6 | 18 | 29.0 | 39.3 | 31.8 |
| 2GOX.pdb | A:B | OX | -12.1 | -11.3 | SPR | 0.6 | 1631 | 13 | 6 | 17 | 3 | 19 | 6 | 30.5 | 35.6 | 33.9 |
| 2HQS.pdb | A:H | OX | -10.2 | -12.1 | ITC | 1.1 | 2333 | 10 | 21 | 37 | 5 | 17 | 19 | 33.2 | 43.9 | 22.9 |
| 2HRK.pdb | A:B | OX | -11 | -8.7 | SPR | 2.0 | 1595 | 8 | 11 | 14 | 1 | 9 | 13 | 32.5 | 40.3 | 27.3 |
| 2I25.pdb | N:L | A | -12.3 | -12.0 | SPR | 1.2 | 1425 | 7 | 7 | 17 | 2 | 18 | 13 | 39.1 | 31.8 | 29.1 |
| 2MTA.pdb | HL:A | ES | -7.4 | -7.8 | spectroscopy | 0.4 | 1461 | 3 | 3 | 21 | 2 | 11 | 24 | 24.5 | 45.8 | 29.7 |
| 2NYZ.pdb | AB:D | OR | -12.7 | -12.7 | SPR | 2.1 | 2160 | 6 | 10 | 18 | 5 | 25 | 20 | 38.5 | 36.4 | 25.1 |
| 2OOB.pdb | A:B | ES | -5.7 | -6.2 | ITC | 0.8 | 808 | 3 | 3 | 13 | 0 | 2 | 15 | 27.2 | 34.8 | 38.0 |
| 2PCB.pdb | A:B | NC | -6.8 | -7.4 | ITC | 0.5 | 1029 | 11 | 4 | 7 | 3 | 7 | 1 | 30.9 | 35.4 | 33.8 |
| 2PCC.pdb | A:B | ES | -7.9 | -8.1 | ITC | 0.4 | 1141 | 8 | 6 | 5 | 2 | 10 | 8 | 32.8 | 34.7 | 32.5 |
| 2TGP.pdb | Z:I | NC | -7.5 | -12.3 | spectroscopy | 0.6 | 1432 | 4 | 9 | 28 | 1 | 14 | 20 | 43.0 | 38.6 | 18.4 |
| 2VIR.pdb | AB:C | A | -12.3 | -10.9 | SPR | 0.8 | 1263 | 0 | 5 | 8 | 9 | 25 | 12 | 43.2 | 38.0 | 18.8 |
| 2VIS.pdb | AB:C | NC | -7.4 | -11.0 | SPR | 0.8 | 1296 | 0 | 5 | 8 | 7 | 23 | 16 | 43.7 | 37.9 | 18.4 |
| 2WPT.pdb | A:B | NC | -10.7 | -11.9 | stopped-flow | 1.6 | 1581 | 8 | 14 | 12 | 2 | 28 | 10 | 23.1 | 27.2 | 49.7 |
| 3BZD.pdb | A:B | OX | -9.6 | -9.4 | ITC | 1.1 | 1312 | 4 | 7 | 6 | 7 | 15 | 12 | 41.0 | 29.5 | 29.5 |
| 3CPH.pdb | G:A | OG | -8.8 | -9.3 | ITC | 2.1 | 1685 | 6 | 7 | 14 | 2 | 15 | 19 | 28.8 | 35.7 | 35.5 |
| 3SGB.pdb | E:I | EI | -14.5 | -13.1 | spectroscopy | 0.4 | 1268 | 3 | 5 | 15 | 2 | 20 | 20 | 49.4 | 36.0 | 14.5 |
| 4CPA.pdb | A:I | EI | -11.3 | -10.1 | spectroscopy | 1.5 | 1177 | 0 | 3 | 16 | 5 | 10 | 19 | 48.0 | 31.7 | 20.4 |
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)
- 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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