ChemLabelMe is a tool used for annotating and correcting the correspondence between chemical structures and chemical information (ID, chemical name, properties) in papers/patents, and has been used…

Auto-QChem is an automated workflow for the generation and storage of DFT calculations for organic molecules.

AIMNet2 hands-on tutorial: nine notebooks from a single-point energy to chemical reactivity. AiMat Summer School 2026, Machine Learning for Molecules

OpenMM/PySCF integration using PythonForce for QM and QM/MM quantum-mechanical modeling

Code used for the OpenADMET CYP competition

Finds cryptic binding pockets that are invisible in a single static structure. Generates a conformational ensemble, detects pockets in every conformer, clusters them into transient sites, and ranks…

Pocket-Conditioned Autoregressive 3D Molecular Generation with a Neighborhood-Guided Set Transformer

MOlecule fRagmenTAtion fRamework

Chemistry Development Kit module for scaffold functionalities

Predicting water moelcule placements on protein surfaces using flow matching conditioned on learned protein structure embeddings.

Molecular dynamics simulation skills for AI agents

Benchmark for LLM-agent molecular dynamics, scored against public MDDB reference simulations

Enable cheminformatics and quantum chemistry

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 190,000+ scientists worldwide. 165 ready-to-use validated skills plus 100+ scientific databases covering bio…

De novo Design of Macrocyclic Molecular Glues

PyTorch operations for use in creating machine learning interatomic potentials

NACraft for programmatic aptamer design

The open-source AI research workbench for scientific research and agent workflows. Local-first, model-agnostic desktop app with extensible skills, MCP tools and connectors, Python/R execution and t…

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

A community collection of bioinformatic analyses for anyone to learn and adapt

Pretraining non-canonical amino acids

Built by DeepSeek, for DeepSeek — a Swift-native macOS coding agent

Code for "Strategy-first synthesis planning for complex natural products"

qFit: Automated and unbiased multi-conformer models from X-ray and EM maps.

Local UI to run and train LLMs and diffusion models. Supports GGUF, MLX, Qwen3.8, DeepSeek-V4, MiniMax-H3, Gemma 4, FLUX and more.

macOS desktop app and Quick Look extension for molecular previews: Mol* 3D, xyzrender SVG, and RDKit grids.

ARCHIVED legacy compatibility bridge. Active development continues at SergeiNikolenko/Burette.