## 2 Results and Discussion
### Discrimination with Interaction Energy  
In the next step we were interested in investigating whether it is possible to select the native protein-protein interaction from a set of possible solutions. For this purpose we analyzed enzyme-inhibitor interactions for which the corresponding structures of the free proteins as well as the structures of the native complexes were available [9]. For each test case several putative inhibitors were docked to the known interaction site of one given enzyme employing again the HADDOCK docking algorithm. As detailed in the methods section average interaction energies, which are the sum of van der Waals energies and electrostatic energies between intermolecular atom-pairs were calculated for the 10 finally selected complex structures of each docking run. \begin{table}
\begin{tabular}{l|l|l|l|l|l} \hline
**Receptor** & **Ligand** & \({}^{*}E_{\text{int}}=E_{\text{vdw}}+E_{\text{dse}}\) & \({}^{*}E_{\text{int}}=E_{\text{vdw}}+E_{\text{dse}}\) & \({}^{*}\)**Rank** \\  & & **[kJ/mol]** & **[kJ/mol]** & **[kJ/mol]** \\ \hline Barnase & Barstar & 913.2 & -142.5 & \\ Barnase & Soybean trypsin inhibitor & -670.0 & -1173.9 & 2 \\ Barnase & Ovomucoid 3 rd domain & -575.0 & -481.3 & 3 \\ Barnase & Eglin C & -510.6 & -546.6 & 4 \\ Barnase & Pancreatic secretory trypsin inhibitor & -504.7 & -910.7 & 5 \\ Barnase & APPI & -481.3 & -301.3 & 6 \\ \(\alpha\)-Chymotrypsin & Eglin C & 552.8 & 367.9 & \\ \(\alpha\)-Chymotrypsin & Barstar & -505.5 & -341.5 & 2 \\ \(\alpha\)-Chymotrypsin & APPI & -445.7 & -307.6 & 3 \\ \(\alpha\)-Chymotrypsin & Soybean trypsin inhibitor & -364.9 & -469.1 & 4 \\ \(\alpha\)-Chymotrypsin & Pancreatic secretory trypsin inhibitor & -306.3 & -397.2 & 5 \\ Bovine trypsin & CMTI-1 squash inhibitor & 588.4 & 737.4 & \\ Bovine trypsin & Glycosylase inhibitor & -761.3 & -876.3 & 1 \\ Bovine trypsin & RAGI inhibitor & -492.2 & -565.0 & 3 \\ Bovine trypsin & Soybean trypsin inhibitor & -436.5 & -513.5 & 4 \\ Bovine trypsin & _Streptomyces_ subtilisin inhibitor & -412.6 & -509.7 & 5 \\ Bovine trypsin & Amicyanin & -323.9 & -352.4 & 6 \\ \hline \end{tabular}
\end{table} 
Table 1: Comparison of intermolecular interaction energies of native (shaded in gray) and corresponding non-native complexes. \({}^{*}\)The energy is always the average of ten complexes that were top ranked from the docking algorithm. \({}^{\text{b}}\)The interaction energy of the complex top ranked by the docking algorithm is shown. \({}^{\text{c}}\)Results are ranked according to the average interaction energies provided in the third column. We investigated the potential of these interaction energies to discriminate between native and non-native interactions. In the following we will show three typical example test cases. The first one is again Barnase and its interactions with a set of putative inhibitors. We docked Barstar (the native inhibitor), soybean trypsin inhibitor, APPI, Ovomucoid 3 rd domain and Pancratic secretory trypsin inhibitor (inhibitors that do not interact with Barnase) to Barnase. As can be seen on the bottom part of Figure 1 and on the top and bottom part of Figure 2 the structure with the lowest HADDOCK score is not necessarily the best one (smallest RMSD to the native structure). Therefore, to include at least some near native structures in the analysis, we always calculated the mean interaction energies for the 10 selected structures of every docking run and compared these mean values to each other. The results for Barnase and two similar tests with \(\alpha\) - Chymotrypsin and _Bovine_ trypsin can be seen in Table 1. For reasons of comparison the interaction energy obtained for the top ranked structure of each docking run is displayed in the second last column of the table. Note that these structures do not necessarily possess the best interaction energy since the ranking within a docking run is based on calculated scores and not solely on interaction energies.