| Crosbi ID | 849334 |
| Year | 2024 |
| Status | Objavljeno |
| Type | prilog u časopisu |
| Subtype | izvorni znanstveni rad |
| Authors | Gomaz, Boris; Pandini, Alessandro; Maršavelski, Aleksandra; Štefanić, Zoran |
| Journal | Journal of chemical information and modeling |
| Volume | 64 |
| Issue | 15 |
| Pages | str. 5742-5748 |
| DOI | 10.1021/acs.jcim.4c00650 |
| ISSN | 1549-9596 |
| EISSN | 1549-960X |
en original MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams
Extracting meaningful information from atomistic molecular dynamics (MD) simulations of proteins remains a challenging task due to the high-dimensionality and complexity of the data. MD simulations yield trajectories that contain the positions of thousands of atoms in millions of steps. Gaining a comprehensive understanding of local dynamical events across the entire trajectory is often difficult. Here, we present a novel approach to visualize MD trajectories in the form of time-dependent Ramachandran plots. Specialized data aggregation techniques are employed to address the challenge of plotting millions of data points on a single image, thereby ensuring that the analysis is independent of the molecule size and/or length of the MD simulation. This approach facilitates quick identification of flexible and dynamic regions, and its strength is the ability to simultaneously observe the movements of all amino acids over time. The Python program MDavocado is freely available at GitHub (https://github.com/zoranstefanic/MDavocado).
en original Computational chemistry; Conformation; Monomers; Peptides and proteins; Protein structure
Gomaz, Boris; Pandini, Alessandro; Maršavelski, Aleksandra; Štefanić, Zoran MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams // Journal of chemical information and modeling, 64 (2024), 15; 5742-5748. doi: 10.1021/acs.jcim.4c00650
Medline Scopus Web of Science Core Collection, SCI-Exp, SSCI & A&HCI (WoSCC-SCI-Exp, SSCI, A&HCI) Web of Science Core Collection, Science Citation Index Expanded (WoSCC-SCI-Exp)