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OpenMM is a molecular simulation toolkit. Its official OpenMM-ML extension connects machine learning potentials to simulations.

Computational Chemistry

e3nn provides mathematical components for E(3)-equivariant networks, including representations, tensor products and spherical harmonics.

PyTorch Geometric (PyG) is a general graph neural network library with an official QM9 example for molecular property learning.

Molecular Property Prediction

DGL-LifeSci is a DGL/PyTorch toolkit providing graph learning components and examples for chemistry and biology.

Molecular Property Prediction

ASE is a Python atomistic simulation library connecting conventional codes and external machine learning potentials through a common calculator interface.

Computational Chemistry

Academic platform for managing and exploring materials research data, with notebook-based analysis through the NOMAD AI Toolkit.

Materials Discovery · Scientific Data

Academic materials data platform for exploring computed structures and properties and preparing materials-discovery research.

Materials Discovery · Scientific Data

This ESM entry covers the Meta FAIR repository, including ESM-2 protein representations and ESMFold structure prediction.

ProteinMPNN designs amino-acid sequences from protein backbones and provides full-backbone and Cα-only models.

RFdiffusion is a protein backbone diffusion project supporting unconditional generation, motif constraints and binder design.

Molecular Generation

OpenFold is a trainable PyTorch implementation of AlphaFold 2 for protein structure inference and training.

Boltz is a biomolecular interaction model family. Boltz-2 provides workflows for complex structure and binding affinity prediction.

Drug Discovery

SevenNet provides graph neural network interatomic potentials, pretrained models, fine-tuning interfaces and ASE/LAMMPS integration.

Computational Chemistry

MatGL is a materials graph learning library for developing and using property predictors and machine learning potentials.

Computational Chemistry · Materials Discovery

AIDDISON Explorer is a hosted drug-discovery platform that generates and ranks molecular candidates against target profiles, design constraints, predicted properties and synthetic feasibility.

Molecular Generation · Drug Discovery

Rowan is a cloud platform for molecular calculations, combining quantum chemistry, machine-learned potentials, property prediction, and protein–ligand workflows through a web interface and Python API.

Computational Chemistry · Quantum Chemistry

RCSB PDB Data API provides REST and GraphQL access to structure metadata, molecular sequences, chemical descriptors, and annotations for PDB entries and selected computed structure models.

Drug Discovery · Scientific Data

PubChem PUG REST is an HTTP API for retrieving selected chemical records, properties and assay information, with documented identifier inputs, structure searches and operation-specific output formats.

Cheminformatics · Scientific Data

An instruction Skill for using rdkit-agent in cheminformatics workflows, emphasizing chemical-string validation, structured JSON exchange, bounded outputs and documented RDKit WASM limitations.

Cheminformatics

A reactive-MD post-processing Skill that guides ReacNetGenerator tool selection, LAMMPS trajectory preparation, reaction-network generation and inspection of existing analysis outputs.

Computational Chemistry