Methods of identification and Visualization of Tunnels for Flexible Ligands in Dynamic Proteins

supported by GACR, grant No. 17-07690S

 

Partner Research topics Key persons Web

University of West Bohemia, Faculty of Applied Sciences, Plzen, Czech Republic (UWB)

extraction of spatial information, efficient data representation

prof. Ivana Kolingerova, Ing. Martin Manak, Ph.D.

Link 

Masaryk University, Faculity of Informatics, Brno, Czech Republic (MUNI)

visualization

RNDr. Barbora Kozlikova, Ing. Adam Jurcik, Ph.D.

Link

Czech Technical University in Prague, Faculty of electrical engineering, Prague, Czech Republic (CVUT)

motion planning

Ing. Martin Saska, Dr. rer. nat., Ing. Vojtech Vonasek, Ph.D.

Link

 

Proteins are biochemical macromolecules perforrming crucial functions in all living organisms. Understanding protein 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 project aims to develop computational and visualization methods based on motion planning. The methods will work for flexible ligands moving in dynamic proteins.

 
Objectives:
Efficient extraction of spatial information to guide sampling of configuration space of a flexible ligand moving in a dynamic protein (UWB)
Motion planning using this spatial information (CVUT)
Visualization of ligand movement (MUNI)
 
 
Example of an active site (denoted by the arrow)   Examples of spherical tunnels (accessible pathways) leading towards the active site An example of a single trajectory inside one of these tunnels for a ligand
Publications:
  1. V Vonasek and B Kozlikova. Tunnel detection in protein structures using sampling-based motion planning. In 2017 11th International Workshop on Robot Motion and Control (RoMoCo). July 2017, 185-192. PDF, DOI BibTeX

    @inproceedings{vonasek2017tunnel,
    	author = "V. Vonasek and B. Kozlikova",
    	booktitle = "2017 11th International Workshop on Robot Motion and Control (RoMoCo)",
    	title = "Tunnel detection in protein structures using sampling-based motion planning",
    	year = 2017,
    	pages = "185-192",
    	doi = "10.1109/RoMoCo.2017.8003911",
    	pdf = "data/papers/romoco2017_vonasek.pdf",
    	month = "July"
    }
    
  2. Vojtech Vonasek and Barbora Kozlikova. Application of sampling-based path planning for tunnel detection in dynamic protein structures. In 2016 21st International Conference on Methods and Models in Automation and Robotics (MMAR). August 2016, 1010-1015. URL PDF, DOI BibTeX

    @inproceedings{vonasek2016application,
    	author = "Vonasek, Vojtech and Kozlikova, Barbora",
    	booktitle = "2016 21st International Conference on Methods and Models in Automation and Robotics (MMAR)",
    	title = "Application of sampling-based path planning for tunnel detection in dynamic protein structures",
    	year = 2016,
    	pages = "1010-1015",
    	keywords = "Atomic measurements;Cavity resonators;Collision avoidance;Probes;Proteins;Robots;Stability analysis",
    	doi = "10.1109/MMAR.2016.7575276",
    	month = "Aug",
    	pdf = "data/papers/mmar2016protein.pdf",
    	url = "http://ieeexplore.ieee.org/document/7575276/"
    }