Robin: A multi-agent system for automating scientific discovery

An aviary-based data science agent based on jupyter notebooks

Official Compound Engineering plugin for Claude Code, Codex, Cursor, and more

A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).

AI Agent Skills for MD analysis

Stable Diffusion web UI

Coarse-grained molecular dynamics for protein physics

Desktop Companion for Hermes Agent

The state of the art Deep CNN neural network for de novo sequencing of tandem mass spectra

Universal Deconvolution of Mass and Ion Mobility Spectra

MS-cleavable search engine that enables interactomic analysis by identifying tandem mass spectra of cross-linked peptides.

A Rust library for peptide centric mass spec calculations centered around PSI standards and handling complex cases robustly

A rust library for parsing Pro Forma peptides and matching them against MS spectra

Generate coarse-grained molecular dynamics models from atomistic trajectories.

Automatic MARTINI parametrization of small organic molecules

The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery 🧑‍🔬

De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Python-side access to PPI data from Gygi lab

Describe and apply transformation on molecular structures and topologies

INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems

Protein Engineering via Exploration of an Energy Landscape

Code for running BinderFlow

Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)

Code for the DISCO model: General Multimodal Protein Design Enables DNA-Encoding of Chemistry