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
- Standard Projects
- MU Faculty or unit
- Faculty of Informatics
- Cooperating Organization
-
University of West Bohemia in Pilsen
- Responsible person prof. Dr. Ing. Ivana Kolingerová
- Responsible person Dr.rer.nat. Martin Saska
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.
Publications
Total number of publications: 5
2019
-
Computing multiple guiding paths for sampling-based motion planning
Proceedings of the 19th International Conference on Advanced Robotics, ICAR 2019, year: 2019
-
DockVis: Visual Analysis of Molecular Docking Data
Eurographics Workshop on Visual Computing for Biology and Medicine, year: 2019
-
Sampling-based Motion Planning for Tracking Evolution of Dynamic Tunnels in Molecular Dynamics Simulations
Journal of Intelligent & Robotic Systems, year: 2019, volume: 93, edition: 3-4, DOI
-
Visual Analysis of Ligand Trajectories in Molecular Dynamics
IEEE Pacific Visualization Symposium 2019, year: 2019
2018
-
CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories
Bioinformatics, year: 2018, volume: 34, edition: 20, DOI