Official repository for the Boltz biomolecular interaction models
- binding-prediction
- drug-discovery
- protein-structure
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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
Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python
- quantum-chemistry
- c-plus-plus
- python
- computational-chemistry
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
- deep-learning
- pytorch
- deep-chemistry
- graph-neural-network
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
An open library for the analysis of molecular dynamics trajectories
- molecular-dynamics
- python
- mdtraj
- rmsd
⚗ A package useful for chemistry written in Python
- chemistry
- physical-chemistry
- chemical-kinetics
- chemical-formulas
Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)
A Euclidean diffusion model for structure-based drug design.
- ddpm
- drug-design
- equivariance
- generative-model
The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)
- ai-for-science
- diffusion-models
- drug-design
- equivariant-networks
Source code for "DeepDTA: deep drug-target binding affinity prediction"
- protein-ligand-interactions
- convolutional-neural-networks
GraphDTA: Predicting drug-target binding affinity with graph neural networks
ChEMBL database structure pipelines
Open Parser for Systematic IUPAC Nomenclature. Chemical name to structure conversion
a unified framework for modeling chemically reactive systems
- chemical-equilibrium
- chemical-kinetics
- reactive-transport
- chemical-reactions
Wrapper for RDKit's RunReactants to improve stereochemistry handling
A script to run structural alerts using the RDKit and ChEMBL
LLM for Drug Editing, ICLR 2024
- chatgpt
- conversation
- drug
- drug-discovery
Chemical 2D structure editor application/applet based on the Chemistry Development Kit
- blueobelisk
- java
- chemistry
CGRs, molecules and reactions manipulation
The d-SEAMS C++ core engine
- molecular-dynamics-simulation
- molecular-dynamics
- trajectory-analysis
- lua
UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.
- benchmark
- bioinformatics
- cheminformatics
- computational-chemistry