MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams

Gomaz, Boris; Pandini, Alessandro; Maršavelski, Aleksandra; Štefanić, Zoran (2024) MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams. Journal of Chemical Information and Modeling, 64 (15). pp. 5742-5748. ISSN 1549-9596

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Abstract

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).

Item Type:	Article
Uncontrolled Keywords:	Computational chemistry; Conformation; Monomers; Peptides and proteins; Protein structure
Subjects:	NATURAL SCIENCES > Chemistry > Physical Chemistry NATURAL SCIENCES > Biology > Biochemistry and Molecular Biology
Divisions:	Division of Physical Chemistry
Projects:	Project title Project leader Project code Project type Alosterički komunikacijski putevi u oligomernim enzimima-ALOKOMP/ALOCOMP Zoran Štefanić; Marko Tomin; Aleksandra Maršavelski; Alessandro Pandini; Bojana Dalbelo-Bašić; Agnieszka Bzowska IP-2019-04-6764 HRZZ Odlazna mobilnost asistenata - Boris Gomaz Boris Gomaz MOBDOK-2023-6223 HRZZ Enzimsko inženjerstvo za održivo recikliranje bioplastike Aleksandra Maršavelski NPOO.C3.2.R2-I1.06.0041 EU
Depositing User:	Dr. Zoran Štefanić
Date Deposited:	16 Dec 2025 12:37
URI:	http://fulir.irb.hr/id/eprint/10528
DOI:	10.1021/acs.jcim.4c00650

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