Open Source
Our Software
Tools built in the Perez group — open, reproducible, and designed to push the boundaries of what computational biology can do.
MELD (Modeling Employing Limited Data) is a framework that integrates sparse and ambiguous experimental data — from NMR, cryo-EM, and cross-linking mass spectrometry — directly into molecular dynamics simulations. It resolves biomolecular structures that neither experiment nor simulation could achieve alone.
MDZip is a neural network-based compression framework designed specifically for molecular dynamics trajectories. It enables scalable storage and high-fidelity reconstruction of large MD ensembles — a core tool powering the MDDBA data infrastructure initiative.
The Molecular Dynamics Databank — America Node is a large-scale, FAIR-compliant repository of MD trajectories. Built to power the next generation of AI models on protein dynamics, it sets a new standard for open, reproducible biomolecular simulation data.
Perez Lab on GitHub
Browse all repositories, datasets, and ongoing projects from the group.
All software developed in the Perez group is open source and freely available. We believe in reproducible science and community-driven development. Contributions and collaborations are welcome — reach out via our contact page or open an issue directly on GitHub.