Therefore, more approaches should be explored in order to improve the prediction accuracy of scoring functions for more reliable protein protein docking.
As more receptor-type specific data is available, however, these models will continue to evolve to capture individual conformational preferences for the receptors leading to more reliable automated docking and virtual screens.
In our procedure, we are (i) using a high-resolution X-ray structure from the MHC of interest, which we will call 'MHC donor', (ii) fitting the target epitope backbone to an allele-specific pattern conformation (previously determined) and (iii) using a reliable molecular docking software (19) to identify the best conformation for each epitope's side chain inside the cleft.
Simulation results show that the IDVD-method based guidance system guarantees a reliable and efficient docking process by generating computationally efficient, feasible and ready to be tracked trajectories.
DOI: http://dx.doi.org/10.7554/eLife.03714.020 The 8.9 Å EM map fits remarkably well with crystal structures of TibA55-350 (PDB ID code: 4Q1Q) (Lu et al., 2014) and the TibC dodecamer, allowing for reliable atomic model docking.
The model from Bikadi et al. has not been used to discriminate binders from nonbinders, as they did not consider docking experiments reliable enough.
The root mean square deviation range was 0.0154 0.9753, with all values less than 2 Å, indicating that Surflex-Dock was reliable in causing reappearance of the binding pattern of the ligand, and the parameter setting for molecular docking was appropriate.
AutoDock4 is acknowledged to be one of the most reliable and broadly used molecular docking tool [5], with several examples of accurate docking predictions already published [6, 7].
In our previous study [44], we conducted an in-depth analysis of the capabilities of structure-based molecular docking as a reliable prediction tool for detecting HLA-B*57 01 HLA-B*57 01ounds.
