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PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

Molecular dynamics simulations with an LLM agent

Automatable GenAI Scripting

Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows

Development version of plumed 2

Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

Chromium running inside your terminal

User friendly and accurate binder design pipeline

A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some t…

Zotero plugin to automatically move attachments and link them

Minimal AlphaFold

Notebook Personal Wiki

Python interactive dashboards for learning data science

A Python package to interactively compute, analyze and visualize protein allosteric communication (residue interaction) networks and delta-networks.

Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations

Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.

Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes

Neural network potentials based on graph neural networks and equivariant transformers

📝 Pytest plugin for testing notebooks

Consensus sequences for each Pango lineage

Plot spike differences among SARS-CoV-2 Pango clades

A tiling window manager for macOS based on binary space partitioning

Input files for the protein-ligand benchmark performed with the Alchemical Transfer Method (ATM)