drug-discovery

There are 95 repositories under drug-discovery topic.

NVIDIA / DeepLearningExamples
State-of-the-Art Deep Learning scripts organized by models - easy to train and deploy with reproducible accuracy and performance on enterprise-grade infrastructure.
computer-vision deep-learning drug-discovery forecasting large-language-models mxnet paddlepaddle pytorch recommender-systems speech-recognition speech-synthesis tensorflow tensorflow2 translation nlp
Language:Jupyter Notebook 12931
deepchem / deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
drug-discovery quantum-chemistry deep-learning biology materials-science hacktoberfest
Language:Python 5266
chemprop / chemprop
Message Passing Neural Networks for Molecule Property Prediction
chemistry drug-discovery machine-learning neural-networks
Language:Python 1612
DeepGraphLearning / torchdrug
A powerful and flexible machine learning platform for drug discovery
pytorch deep-learning graph-neural-networks drug-discovery
Language:Python 1412
graphein
a-r-j / graphein
Protein Graph Library
protein protein-structure deep-learning pytorch graph-neural-networks dgl computational-biology bioinformatics structural-biology protein-data-bank protein-design geometric-deep-learning pytorch-geometric python interactomics interactome rna ppi-networks gene-regulatory-networks drug-discovery
Language:Jupyter Notebook 994
mims-harvard / TDC
Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science
machine-learning therapeutics drug-discovery datasets biology chemistry biomedicine bioinformatics cheminformatics deep-learning benchmarks artificial-intelligence precision-medicine medicine biotech
Language:Jupyter Notebook 953
kexinhuang12345 / DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
drug-repurposing deep-learning drug-target-interactions toolkit covid19 virtual-screening drug-discovery ppi ddi dti-prediction drug-property-prediction protein-function-prediction repurposing-drugs qsar side-effects drug-drug-interaction protein-protein-interaction drug-target-interaction bioinformatics
Language:Jupyter Notebook 933
molecularsets / moses
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
benchmark drug-discovery generative-models machine-learning
Language:Python 793
chemicalx
AstraZeneca / chemicalx
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
deep-learning pytorch deep-chemistry graph-neural-network drug drug-pair polypharmacy drug-discovery pharma drug-interaction chemistry biology machine-learning torch geometric-deep-learning geometry smiles smiles-strings torchdrug
Language:Python 700
BioPandas / biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Language:Python 697
awslabs / dgl-lifesci
Python package for graph neural networks in chemistry and biology
bioinformatics cheminformatics deep-learning dgl drug-discovery geometric-deep-learning graph-neural-networks molecule
Language:Python 695
Mariewelt / OpenChem
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
computational-chemistry computational-biology deep-learning deep-neural-networks graph-convolutional-networks drug-discovery drug-design qsar predictive-modeling machine-learning pytorch
Language:Python 667
gnina / gnina
A deep learning framework for molecular docking
cheminformatics computational-chemistry convolutional-neural-networks drug-discovery molecular-modeling
Language:C++ 573
nequip
mir-group / nequip
NequIP is a code for building E(3)-equivariant interatomic potentials
machine-learning atomistic-simulations molecular-dynamics computational-chemistry deep-learning interatomic-potentials force-fields pytorch drug-discovery materials-science
Language:Python 559
HannesStark / EquiBind
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
geometry graph-neural-networks proteins protein-structure drug-discovery molecules equivariance
Language:Python 464
junxia97 / awesome-pretrain-on-molecules
[IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models
awesome chemical-language-models computational-chemistry drug-discovery drug-discovery-and-development finetuning gnns graph-representation-learning molecular-representation-learning molecule self-supervised-learning survey transfer-learning
464
datamol-io / datamol
Molecular Processing Made Easy.
python molecule rdkit drug-discovery drug-design molecules cheminformatics medicinal-chemistry
Language:Python 439
isayev / ReLeaSE
Deep Reinforcement Learning for de-novo Drug Design
deeplearning reinforcement-learning cheminformatics molecular-modeling drug-discovery qsar
Language:Jupyter Notebook 343
chemosim-lab / ProLIF
Interaction Fingerprints for protein-ligand complexes and more
molecular-dynamics rdkit drug-design docking cheminformatics mdanalysis drug-discovery
Language:Python 336
mir-group / allegro
Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials
atomistic-simulations computational-chemistry deep-learning drug-discovery force-fields interatomic-potentials machine-learning materials-science molecular-dynamics pytorch
Language:Python 297
JuDFTteam / best-of-atomistic-machine-learning
🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.
atomistic-machine-learning awesome-list best-of-list computational-chemistry computational-materials-science condensed-matter density-functional-theory drug-discovery electronic-structure interatomic-potentials materials-discovery materials-informatics molecular-dynamics scientific-computing surrogate-models scientific-machine-learning quantum-chemistry ai4science
268
MolecularAI / REINVENT4
AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
ai cheminformatics chemistry denovo-design generative-ai ml molecule-generation astrazeneca deep-learning neural-networks reinforcement-learning transfer-learning drug-design drug-discovery
Language:Python 262
Acellera / htmd
HTMD: Programming Environment for Molecular Discovery
automate drug-discovery htmd molecular-simulations
Language:Rich Text Format 252
AngelRuizMoreno / Jupyter_Dock
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
molecular-docking autodock autodock-vina ledock mdanalysis rdkit openbabel cheminformatics computational-biology jupyter-notebook py3dmol protein protein-structure drug-discovery drug-repurposing drug-design
Language:Jupyter Notebook 248
p2rank
rdk / p2rank
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
binding-sites bioinformatics drug-discovery groovy java ligand machine-learning mmcif molecular-structures p2rank pdb protein-ligand-docking protein-ligand-interactions protein-structure protein-surface proteins pymol random-forest structural-bioinformatics virtual-screening
Language:Groovy 231
octavian-ganea / equidock_public
EquiDock: geometric deep learning for fast rigid 3D protein-protein docking
geometry proteins protein-protein-interaction docking graphneuralnetwork deeplearning equivariant-network equivariance equivariant-representations drugdiscovery drug-discovery
Language:Roff 226
mattragoza / LiGAN
Deep generative models of 3D grids for structure-based drug discovery
deep-learning generative-models drug-discovery protein-structure pytorch molgrid
Language:Python 210
Acellera / moleculekit
MoleculeKit: Your favorite molecule manipulation kit
drug-discovery machine-learning molecular-modeling molecular-simulation molecule proteins
Language:Python 193
ersilia
ersilia-os / ersilia
The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.
ersilia open-source drug-discovery neglected-tropical-disease model-hub python machine-learning
Language:Python 189
chao1224 / MoleculeSTM
Multi-modal Molecule Structure-text Model for Text-based Editing and Retrieval, Nat Mach Intell 2023 (https://www.nature.com/articles/s42256-023-00759-6)
clip computation-chemistry drug-discovery editing pretraining retrieval foundation-model molecule-editing moleculeclip moleculestm
Language:Python 186
pcko1 / Deep-Drug-Coder
A tensorflow.keras generative neural network for de novo drug design, first-authored in Nature Machine Intelligence while working at AstraZeneca.
drug-discovery neural-network denovo-design lstm-neural-networks autoencoders smiles-strings molecules
Language:Python 183
benb111 / awesome-small-molecule-ml
A curated list of resources for machine learning for small-molecule drug discovery
awesome-list machine-learning cheminformatics drug-discovery awesome bioinformatics
182
atomicarchitects / equiformer
[ICLR'23 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs
catalyst-design computational-chemistry deep-learning drug-discovery equivariant-graph-neural-network force-fields interatomic-potentials machine-learning molecular-dynamics pytorch ai-for-science equivariant-neural-networks graph-neural-networks e3nn geometric-deep-learning materials-science
Language:Python 180
AstraZeneca / awesome-drug-discovery-knowledge-graphs
A collection of research papers, datasets and software related to knowledge graphs for drug discovery. Accompanies the paper "A review of biomedical datasets relating to drug discovery: a knowledge graph perspective" (Briefings in Bioinformatics, 2022)
awesome-list drug-discovery drug-discovery-knowledge-graph knowledge-graph
179
MinkaiXu / GeoLDM
Geometric Latent Diffusion Models for 3D Molecule Generation
deep-generative-model diffusion-models drug-discovery geometric-deep-learning icml-2023 molecule molecule-generation
Language:Python 179
choderalab / yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
alchemical alchemical-free-energy-calculations drug-discovery free-energy free-energy-perturbation molecular-dynamics molecular-dynamics-simulation mskcc openmm python
Language:Python 173