Computational protocol: Prediction of protein-binding areas by small-world residue networks and application to docking

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Protocol publication

[…] We used the standard protein-protein docking benchmark 3.0 [] for (i) the assessment of the use of network-based parameters for binding site prediction, (ii) the comparison of the different topological parameters for docking scoring, and (iii) the training of the optimal balance between pyDock and the network-based scoring. The new cases in benchmark 4.0 (the latest so far) [] were used to validate the optimal balance found between pyDock and the network-based scoring. Benchmark 4.0 (which includes the cases of benchmark 3.0) was used for the performance analysis. [...] We used FTDock [] with standard parameters (using electrostatics and 0.7 Å grid resolution) to generate 10,000 rigid-body docking poses for the 176 unbound cases of the latest standard protein-protein docking benchmark []. A docking pose was considered a near-native solution if its ligand Cα-RMSD with respect to the crystal structure was below 10 Å. The success rate for the top 10 predictions was calculated as the percentage of cases in the benchmark that had a near-native solution within the first 10 predictions. For this calculation, only the cases for which FTDock generated at least one near-native solution were considered (103 for benchmark 3.0 and 141 for benchmark 4.0). […]

Pipeline specifications

Software tools pyDock, FTDock
Application Protein interaction analysis