DynamiSpectra: A Python Software Package and Web Platform for Molecular Dynamics Data Analysis in Computational Biology
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...
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2025
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| Summary: | 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. |
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