Repository Index

Official repository for the Boltz biomolecular interaction models

• binding-prediction
• drug-discovery
• protein-structure

Public development project of the LAMMPS MD software package

• molecular-dynamics
• lammps
• simulation
• kokkos

Message Passing Neural Networks for Molecule Property Prediction

• machine-learning
• chemistry
• neural-networks
• drug-discovery

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

• drug-repurposing
• deep-learning
• drug-target-interactions
• toolkit

Molecular Processing Made Easy.

• python
• molecule
• rdkit
• drug-discovery

Source code for "DeepDTA: deep drug-target binding affinity prediction"

• protein-ligand-interactions
• convolutional-neural-networks

Wrapper for RDKit's RunReactants to improve stereochemistry handling

ChemML is a machine learning and informatics program suite for the chemical and materials sciences.

• quantum-mechanics
• materials-informatics
• data-science
• machine-learning

LLM for Drug Editing, ICLR 2024

• chatgpt
• conversation
• drug
• drug-discovery

The Massively Parallel Quantum Chemistry program, MPQC, computes properties of atoms and molecules from first principles using the time independent Schrödinger equation.

Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

• alphafold3
• docking
• drug-design
• drug-discovery

UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.

• benchmark
• bioinformatics
• cheminformatics
• computational-chemistry

Generative models for transcriptomic-driven or protein-driven molecular design (PaccMann^RL).

• deep-reinforcement-learning
• generative-model
• vae
• molecule-generation