  Here we present a novel method for the analysis of transport processes in
proteins and its implementation called CaverDock. Our method is based on a
modified molecular docking algorithm. It iteratively places the ligand along
the access tunnel in such a way that the ligand movement is contiguous and the
energy is minimized. The result of CaverDock calculation is a ligand trajectory
and an energy profile of transport process. CaverDock uses the modified docking
program Autodock Vina for molecular docking and implements a parallel heuristic
algorithm for searching the space of possible trajectories. Our method lies in
between the geometrical approaches and molecular dynamics simulations. Contrary
to the geometrical methods, it provides an evaluation of chemical forces.
However, it is far less computationally demanding and easier to set up compared
to molecular dynamics simulations. CaverDock will find a broad use in the
fields of computational enzymology, drug design and protein engineering. The
software is available free of charge to the academic users at
https://loschmidt.chemi.muni.cz/caverdock/.
