Molecular docking is a computational method for predicting the optimal pose
of one molecule in the binding site of another. In our work, we focused on
improving the open source tool CmDock by upgrading the existing PLP scor-
ing function to CHEMPLP. The main focus was the inclusion of the effects
of hydrogen bonds in the simulation. Despite the use of a more complex
model, the accuracy of the scoring function did not improve, as on the DUD-
E test set, docking with the PLP and CHEMPLP scoring functions reached
an average RMSD of around 9 Å. The maximum accuracy is still achieved by
the default scoring function of the CmDock tool, VDW, while the docking
time with the PLP or CHEMPLP scoring functions is approximately twice
as short. This finding suggests potential for use in high-performance virtual
screening where speed is critical.
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