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Journal of Chemical Information and Modeling
Article . 2025 . Peer-reviewed
License: CC BY
Data sources: Crossref
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PubMed Central
Other literature type . 2025
License: CC BY
Data sources: PubMed Central
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DynamiSpectra: A Python Software Package and Web Platform for Molecular Dynamics Data Analysis in Computational Biology

Authors: Iverson Conrado Bezerra; Jéssika de Oliveira Viana; Karen Cacilda Weber; Priscila Gubert;

DynamiSpectra: A Python Software Package and Web Platform for Molecular Dynamics Data Analysis in Computational Biology

Abstract

Molecular dynamics (MD) simulations generate extensive data sets that demand reliable and reproducible analysis tools. In this study, we present DynamiSpectra, a Python-based software package and web platform designed to automate the descriptive statistical analysis (mean and standard deviation) and visualization of MD trajectories. DynamiSpectra enables streamlined processing of GROMACS-generated files, supporting comparative analyses across multiple simulation replicas without requiring topology file handling or programming expertise. The package performs key structural and dynamic analyses, including RMSD, RMSF, radius of gyration, SASA, hydrogen bonds, salt bridges, secondary structure probability and fraction, principal component analysis, and ligand occupancy maps, producing high-quality graphical outputs with integrated descriptive statistical analysis. Additionally, it supports analyses such as protein-ligand contacts, protein-ligand minimum distance, protein-ligand hydrophobic contacts, inter-residue distance matrices, phi and psi angles, rotamers (χ1 and χ2), ligand dihedral angles, as well as analyses of pressure, temperature, and density within the system. Comparative tests performed against widely used MD analysis packages revealed that the results generated by DynamiSpectra were consistent with those tools. DynamiSpectra stands out for its ability to automate the analysis of multiple replicas, as well as the calculation of mean and standard deviation, which other packages often lack in automation. A use case involving β-amyloid peptide simulations at different temperatures illustrates the platform's capabilities. Furthermore, the DynamiSpectra web interface enables users to upload data, generate interactive plots, and explore results without requiring local installation, thereby promoting accessible and reproducible MD analysis, being another essential distinguishing feature of the tool. The software is freely available via PyPI (https://pypi.org/project/DynamiSpectra/) and GitHub (https://github.com/Conradoou/DynamiSpectra/tree/main). The online web server can be accessed at: https://dynamispectra.onrender.com.

Keywords

Data Analysis, Internet, Application Note, Computational Biology, Proteins, Molecular Dynamics Simulation, Ligands, Software

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
2
Average
Average
Average
Green
hybrid