NumPy
The fundamental foundation for scientific computing and multi-dimensional array processing in Python.

The industry-standard Python library for high-performance molecular dynamics trajectory analysis.
MDAnalysis is an object-oriented Python library designed for the analysis of molecular dynamics (MD) trajectories from various simulation packages including GROMACS, CHARMM, AMBER, NAMD, and OpenMM. In the 2026 research landscape, it stands as the critical middleware for biophysical data science, enabling researchers to manipulate atomistic coordinate data with NumPy-like syntax. The architecture is built around a 'Universe' object that encapsulates both topology and trajectory data, allowing for seamless iteration over frames without loading entire datasets into memory. Its performance is optimized via Cython and integration with high-performance computing (HPC) frameworks like Dask for parallelized analysis. As AI-driven protein folding and drug discovery pipelines have proliferated, MDAnalysis has evolved to serve as the primary data preprocessing engine for training graph neural networks (GNNs) and structural transformers, providing the necessary bridge between raw simulation binaries and machine-learning-ready tensors. It remains free and open-source under the GNU General Public License, supported by a robust global community of developers and scientists.
A sophisticated, SQL-like query language for selecting subsets of atoms based on properties, distance, or geometric constraints.
The fundamental foundation for scientific computing and multi-dimensional array processing in Python.
The world's first AI-driven VR mathematical modeling and vector field simulation engine.
A high-performance C/C++ library and command-line suite for device-independent 2D vector graphics and data plotting.
The gold standard in visual data discovery and interactive statistical modeling for R&D and manufacturing.
Verified feedback from the global deployment network.
Post queries, share implementation strategies, and help other users.
Processes trajectory frames sequentially without loading the entire multi-terabyte file into RAM.
A unified data structure that treats topology and coordinates as a single entity, regardless of the source MD engine.
A library of pre-built, optimized algorithms for common tasks like RMSD, RDF, and PCA.
Native support for distributed computing to parallelize analysis over clusters.
Allows real-time modification of coordinates (e.g., centering, PBC wrapping) during the analysis loop.
Direct conversion to RDKit, Pandas, and NetworkX objects.
Measuring the residence time and distance stability of a drug candidate within a binding pocket over a 1-microsecond simulation.
Registry Updated:2/7/2026
Plot results using Matplotlib.
Characterizing the local thickness and curvature of a complex multicomponent cell membrane.
Quantifying the number of water molecules within 3 Angstroms of a catalytic site.