The pathway of ligands through protein channels and tunnels have been of utmost importance in proteomic studies. It has almost been a daunting task to analyze the binding and unbinding of ligands to the protein molecules.The softwares available for molecular docking are time consuming and computationally demanding.
Recently, Vavra O.et al.(2019) have developed a software for analyzing moecular docking which takes only a few minutes to few hours. In their article they have done a comparison of their method with the already existing methods. They have also analyzed the robustness of their method with ensembles of ligands.They have also done a comparison with trajectories of ligands in engineered tunnels.
Binaries and web implementation of the program is available at the following URLs: https://loschmidt.chemi.muni.cz/caverdock/ and https://loschmidt.chemi.muni.cz/caverweb/ respectively.
Reference:
Vavra O. et. al. (2019) CaverDock: a molecular docking based tool to analyze ligand transport through protein tunnels and channels. Bioinformatics 35(23):4986-4993.