A new method and softare tool for simulation of transport processes in proteins

Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University

Understanding protein-ligand interactions is crucial in many biochemical disciplines, such as drug design or enzyme engineering. In project of Grant Agency of Masaryk University (MUNI/M/1888/2014), we are developing a novel method and tool for analysis of transport processes. Our method uses modified molecular docking based on Autodock Vina, which docks a ligand using constraints allowing precise definition of the position in the protein cavity. By iterative docking of the ligand along the protein cavity, we obtain its trajectory and also energy profile. We use heuristic algorithm to determine the constraints for molecular docking, thus much less protein-ligand conformations are evaluated than in the case of molecular dynamics, resulting in faster simulation.

Our method is being implemented in CaverDock tool, which uses geometrical tunnels from well-known software Caver [Chovancova 2012] as an input and docks a ligand into the tunnel by using our modified docking algorithm. The CaverDock is very easy to setup and needs significantly less computational time comparing to methods based on molecular dynamics, whereas it is still able to return trajectory of ligand movement and energetic profile of the transport process.

Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, et al. (2012) CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Comput Biol 8(10): e1002708. doi:10.1371/journal.pcbi.1002708

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