Project information

Methods of Identification and Visualization of Tunnels for Flexible Ligands in Dynamic Proteins (FLigComp)

Project Identification
GA17-07690S
Project Period
1/2017 - 12/2019
Investor / Pogramme / Project type
Czech Science Foundation
MU Faculty or unit
Faculty of Informatics
Cooperating Organization
Czech Technical University Prague
Responsible person Dr.rer.nat. Martin Saska
University of West Bohemia in Pilsen
Responsible person Prof. Dr. Ing. Ivana Kolingerová
Investor logo

Proteins are biochemical macromolecules, performing crucial functions in all living organisms. Understanding their function is important for faster invention of new drugs and other chemical compounds. Protein functions are highly influenced by their reactivity with other molecules (ligands). Performing a spatial analysis of ligands behavior in proteins under molecular dynamics is one of the most important current tasks in bioinformatics. Current approaches are mostly based on geometry, using a set of spheres and 3D geometrical subdivision. They work well for static models and simple molecules but for dynamic and complex molecular structures are not strong enough. Promising alternative solutions, utilizing sampling-based motion planning approaches, have appeared but sample the configuration space blindly, i.e. using uniform samples. The proposed project aims to develop computational and visualization methods based on a motion planning approach and a more sophisticated sampling. The methods will work for general ligands moving in dynamic proteins.

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