A deep learning package for many-body potential energy representation and molecular dynamics
- deep-learning
- molecular-dynamics
- deepmd
- lammps
Repository Index
76,855 visible repositories in the index
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Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
- diffusion-models
- docking
- binding
- computational-biology
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
- chemistry
- chemical-data
- cheminformatics
- c-plus-plus
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
WebGL accelerated JavaScript molecular graphics library
- molecular-graphics
- molecular-modeling
- computational-biology
- computational-chemistry
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
Molecular Processing Made Easy.
- python
- molecule
- rdkit
- drug-discovery
Benchmarks for generative chemistry
bert-loves-chemistry: a repository of HuggingFace models applied on chemical SMILES data for drug design, chemical modelling, etc.
- huggingface
- bert
- chemical-modelling
- chemical-smiles-data
Parsers and algorithms for computational chemistry logfiles
- python
- computational-chemistry
- quantum-chemistry
Universal cheminformatics toolkit, utilities and database search tools
- indigo
- bingo
- cheminformatics
- chemistry
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
GraphDTA: Predicting drug-target binding affinity with graph neural networks
Source code for "DeepDTA: deep drug-target binding affinity prediction"
- protein-ligand-interactions
- convolutional-neural-networks
Descriptor computation(chemistry) and (optional) storage for machine learning
ChEMBL database structure pipelines
Wrapper for RDKit's RunReactants to improve stereochemistry handling
A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discovery.
Molecule Validation and Standardization
- rdkit
- python
- chemistry
- cheminformatics
ChemML is a machine learning and informatics program suite for the chemical and materials sciences.
- quantum-mechanics
- materials-informatics
- data-science
- machine-learning
A cheminformatics extension for the SQLAlchemy database toolkit.
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