MDAnalysis is a Python package designed for the rapid analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It addresses the issue of diverse and proprietary trajectory formats by providing a uniform, object-oriented Python interface to raw simulation data. This allows users to write portable and immediately usable code for various biomolecular simulation communities. MDAnalysis supports over 25 file formats, including those from popular software packages like NAMD, Amber, Gromacs, CHARMM, and LAMMPS, as well as the Protein Data Bank (PDB) format. The package is written in Python and Cython, using NumPy arrays for interoperability with the broader scientific Python ecosystem. It has been widely adopted and is actively maintained, with contributions from an international developer community. MDAnalysis is available under the GNU General Public License v2 and is widely used as a foundation for more specialized biomolecular simulation tools. Recent improvements include enhanced performance for large systems, improved data structures, and new analysis algorithms, such as LeafletFinder and Path Similarity Analysis. The package is well-suited for interactive and rapid prototyping in IPython and Jupyter notebooks, and it integrates with other tools like pandas, distributed, FireWorks, and MDSynthesis for advanced analysis and visualization.MDAnalysis is a Python package designed for the rapid analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It addresses the issue of diverse and proprietary trajectory formats by providing a uniform, object-oriented Python interface to raw simulation data. This allows users to write portable and immediately usable code for various biomolecular simulation communities. MDAnalysis supports over 25 file formats, including those from popular software packages like NAMD, Amber, Gromacs, CHARMM, and LAMMPS, as well as the Protein Data Bank (PDB) format. The package is written in Python and Cython, using NumPy arrays for interoperability with the broader scientific Python ecosystem. It has been widely adopted and is actively maintained, with contributions from an international developer community. MDAnalysis is available under the GNU General Public License v2 and is widely used as a foundation for more specialized biomolecular simulation tools. Recent improvements include enhanced performance for large systems, improved data structures, and new analysis algorithms, such as LeafletFinder and Path Similarity Analysis. The package is well-suited for interactive and rapid prototyping in IPython and Jupyter notebooks, and it integrates with other tools like pandas, distributed, FireWorks, and MDSynthesis for advanced analysis and visualization.