Master student Matej Kožić and researcher Branimir Bertoša, both from the Chemistry Department, have published the scientific publication: Trajectory maps: molecular dynamics visualization and analysis. The paper was published in the prestigious journal NAR Genomics and Bioinformatics (IF = 4.41).
The published paper introduces a new method for the analysis of molecular dynamics simulations called "Trajectory Maps." In this method, the trajectory obtained from molecular dynamics simulations is analyzed by representing changes in the coordinates of protein backbone atoms during the simulation using heat maps. This novel method effectively complements existing quantitative trajectory analysis methods, and a significant advantage is its ability to identify even subtle conformational changes occurring during the simulation. Additionally, trajectory maps allow for the simultaneous analysis of multiple simulations, facilitating the identification of differences in the structural and dynamic properties of different systems of interest. The application of this new method has been demonstrated on three systems previously explored using existing trajectory analysis methods, highlighting the main advantages of trajectory maps over existing methods. The "trajectory maps" method is publicly available and free to use.
The published results were obtained as part of research conducted within the Croatian Science Foundation project "Manganese Metallosensors" (IP-2020-02-3446) and represent the core of the master's thesis of student Matej Kožić, conducted under the supervision of Branimir Bertoša.
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