Abstract
BackgroundProtein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex process, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter and impasses. This prevents understanding of the ligand transportation and reasoning behind its behavior along the path.ResultsTo address the needs of the domain experts we design an explorative visualization solution based on a multi-scale simplification model. It helps to navigate the user to the most interesting parts of the ligand trajectory by exploring different attributes of the ligand and its movement, such as its distance to the active site, changes of amino acids lining the ligand, or ligand “stuckness”. The process is supported by three linked views – 3D representation of the simplified trajectory, scatterplot matrix, and bar charts with line representation of ligand-lining amino acids.ConclusionsThe usage of our tool is demonstrated on molecular dynamics simulations provided by the domain experts. The tool was tested by the domain experts from protein engineering and the results confirm that it helps to navigate the user to the most interesting parts of the ligand trajectory and to understand the ligand behavior.
Highlights
Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades
A proper understanding of the processes occurring when two or more molecules react helps in the design of new chemical matters, e.g., in drug design or protein engineering
We aim to provide the domain experts with a tool for intuitive and interactive exploration of already captured molecular dynamics (MD) simulation containing the process of ligand binding
Summary
Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The researchers aim to combine a protein with a given ligand in order to design a new drug or to change protein properties and their function. In these particular cases the ligand has to be transported from the outer solvent to the protein active site where the chemical reaction between the ligand and the amino acids surrounding the active site takes place. As the active site is usually buried deeply in the protein structure and inaccessible directly from its surface, the ligand has to find a suitable transportation path through the protein structure This process, called molecular docking, is very complex, lengthy, and its analysis is heavy on computational resources.
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