Topic: drug-discovery Goto Github

👇 Here are 557 public repositories matching this topic...

a-r-j / graphein
drug-discovery,Protein Graph Library
User: a-r-j
Home Page: https://graphein.ai/
protein protein-structure deep-learning pytorch graph-neural-networks dgl computational-biology bioinformatics structural-biology protein-data-bank

acellera / htmd
drug-discovery,HTMD: Programming Environment for Molecular Discovery
Organization: acellera
Home Page: https://software.acellera.com/docs/latest/htmd/index.html
automate drug-discovery htmd molecular-simulations

acellera / moleculekit
drug-discovery,MoleculeKit: Your favorite molecule manipulation kit
Organization: acellera
drug-discovery machine-learning molecular-modeling molecular-simulation molecule proteins

angelruizmoreno / jupyter_dock
drug-discovery,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.
User: angelruizmoreno
molecular-docking autodock autodock-vina ledock mdanalysis rdkit openbabel cheminformatics computational-biology jupyter-notebook

astrazeneca / awesome-drug-discovery-knowledge-graphs
drug-discovery,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)
Organization: astrazeneca
Home Page: https://academic.oup.com/bib/article-abstract/23/6/bbac404/6712301
drug-discovery knowledge-graph awesome-list drug-discovery-knowledge-graph

astrazeneca / chemicalx
drug-discovery,A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
Organization: astrazeneca
Home Page: https://chemicalx.readthedocs.io
deep-learning pytorch deep-chemistry graph-neural-network drug drug-pair polypharmacy drug-discovery pharma drug-interaction

atomicarchitects / equiformer
drug-discovery,[ICLR'23 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs
Organization: atomicarchitects
Home Page: https://arxiv.org/abs/2206.11990
catalyst-design computational-chemistry deep-learning drug-discovery equivariant-graph-neural-network force-fields interatomic-potentials machine-learning molecular-dynamics pytorch

atomicarchitects / equiformer_v2
drug-discovery,[ICLR'24] EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations
Organization: atomicarchitects
Home Page: https://arxiv.org/abs/2306.12059
catalyst-design computational-chemistry computational-physics deep-learning drug-discovery equivariant-graph-neural-network equivariant-neural-networks force-fields interatomic-potentials machine-learning

awslabs / dgl-lifesci
drug-discovery,Python package for graph neural networks in chemistry and biology
Organization: awslabs
bioinformatics cheminformatics deep-learning dgl drug-discovery geometric-deep-learning graph-neural-networks molecule

benb111 / awesome-small-molecule-ml
drug-discovery,A curated list of resources for machine learning for small-molecule drug discovery
User: benb111
awesome awesome-list bioinformatics cheminformatics drug-discovery machine-learning

benevolentai / deeplytough
drug-discovery,DeeplyTough: Learning Structural Comparison of Protein Binding Sites
Organization: benevolentai
protein-structure drug-discovery deep-learning metric-learning 3d-models

biopandas / biopandas
drug-discovery,Working with molecular structures in pandas DataFrames
Organization: biopandas
Home Page: https://BioPandas.github.io/biopandas/
molecular-structures pandas-dataframe pdb mol2 protein-structure molecules pdb-files drug-discovery computational-biology bioinformatics

blazerye / drugassist
drug-discovery,DrugAssist: A Large Language Model for Molecule Optimization
User: blazerye
Home Page: https://arxiv.org/abs/2401.10334
drug-discovery large-language-models molecule-optimization instruction-datasets ai-for-science instruction-tuning molecule-generation

chao1224 / chatdrug
drug-discovery,LLM for Drug Editing, ICLR 2024
User: chao1224
Home Page: https://chao1224.github.io/ChatDrug
chatgpt conversation drug drug-discovery editing molecule motif peptide protein retrieval secondary-structure small-molecule structure domain-feedback drug-editing chatgpt3 llm

chao1224 / moleculestm
drug-discovery,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)
User: chao1224
Home Page: https://chao1224.github.io/MoleculeSTM
clip computation-chemistry drug-discovery editing pretraining retrieval foundation-model molecule-editing moleculeclip moleculestm

chemosim-lab / prolif
drug-discovery,Interaction Fingerprints for protein-ligand complexes and more
Organization: chemosim-lab
Home Page: https://prolif.readthedocs.io
molecular-dynamics rdkit drug-design docking cheminformatics mdanalysis drug-discovery

chemprop / chemprop
drug-discovery,Message Passing Neural Networks for Molecule Property Prediction
Organization: chemprop
Home Page: https://chemprop.csail.mit.edu
chemistry drug-discovery machine-learning neural-networks

choderalab / yank
drug-discovery,An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Organization: choderalab
Home Page: http://getyank.org
molecular-dynamics molecular-dynamics-simulation alchemical-free-energy-calculations drug-discovery free-energy openmm mskcc python alchemical free-energy-perturbation

datamol-io / datamol
drug-discovery,Molecular Processing Made Easy.
Organization: datamol-io
Home Page: https://docs.datamol.io
python molecule rdkit drug-discovery drug-design molecules cheminformatics medicinal-chemistry

deepchem / deepchem
drug-discovery,Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
Organization: deepchem
Home Page: https://deepchem.io/
drug-discovery quantum-chemistry deep-learning biology materials-science hacktoberfest

deepgraphlearning / torchdrug
drug-discovery,A powerful and flexible machine learning platform for drug discovery
Organization: deepgraphlearning
Home Page: https://torchdrug.ai/
pytorch deep-learning graph-neural-networks drug-discovery

epam / indigo
drug-discovery,Universal cheminformatics toolkit, utilities and database search tools
Organization: epam
Home Page: http://lifescience.opensource.epam.com
indigo bingo cheminformatics chemistry python dotnet postgresql webassembly java molfile

ersilia-os / ersilia
drug-discovery,The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.
Organization: ersilia-os
Home Page: https://ersilia.io
ersilia open-source drug-discovery neglected-tropical-disease model-hub python machine-learning

genular / pandora
drug-discovery,PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:
Organization: genular
Home Page: https://atomic-lab.org
bioinformatics biomarkers clinical-data clustering data-integration data-mining data-science data-visualization drug-discovery genomic-data-analysis machine-learning microbiome pandora predictive-analytics systems-biology transcriptomics tsne umap unsupervised-machine-learning

gnina / gnina
drug-discovery,A deep learning framework for molecular docking
Organization: gnina
convolutional-neural-networks cheminformatics computational-chemistry molecular-modeling drug-discovery

hachmannlab / chemml
drug-discovery,ChemML is a machine learning and informatics program suite for the chemical and materials sciences.
Organization: hachmannlab
Home Page: https://hachmannlab.github.io/chemml
quantum-mechanics materials-informatics data-science machine-learning drug-discovery deep-learning

hannesstark / equibind
drug-discovery,EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
User: hannesstark
geometry graph-neural-networks proteins protein-structure drug-discovery molecules equivariance

isayev / release
drug-discovery,Deep Reinforcement Learning for de-novo Drug Design
User: isayev
deeplearning reinforcement-learning cheminformatics molecular-modeling drug-discovery qsar

judftteam / best-of-atomistic-machine-learning
drug-discovery,🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.
Organization: judftteam
atomistic-machine-learning awesome-list best-of-list computational-chemistry computational-materials-science condensed-matter density-functional-theory drug-discovery electronic-structure interatomic-potentials

junxia97 / awesome-pretrain-on-molecules
drug-discovery,[IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models
User: junxia97
gnns transfer-learning drug-discovery molecule self-supervised-learning survey awesome graph-representation-learning finetuning molecular-representation-learning

kexinhuang12345 / deeppurpose
drug-discovery,A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
User: kexinhuang12345
Home Page: https://doi.org/10.1093/bioinformatics/btaa1005
drug-repurposing deep-learning drug-target-interactions toolkit covid19 virtual-screening drug-discovery ppi ddi dti-prediction

lifanchen-simm / transformercpi
drug-discovery,TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524
User: lifanchen-simm
self-attention compound-protein-interaction transformercpi structure-free-virtual-sreening drug-target-identification drug-discovery

mariewelt / openchem
drug-discovery,OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
User: mariewelt
Home Page: https://mariewelt.github.io/OpenChem/
computational-chemistry computational-biology deep-learning deep-neural-networks graph-convolutional-networks drug-discovery drug-design qsar predictive-modeling machine-learning

matteoferla / fragmenstein
drug-discovery,Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse
User: matteoferla
cheminformatics drug-discovery

mattragoza / ligan
drug-discovery,Deep generative models of 3D grids for structure-based drug discovery
User: mattragoza
deep-learning generative-models drug-discovery protein-structure pytorch molgrid

mims-harvard / tdc
drug-discovery,Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Science
Organization: mims-harvard
Home Page: https://tdcommons.ai
machine-learning therapeutics drug-discovery datasets biology chemistry biomedicine bioinformatics cheminformatics deep-learning

minkaixu / geoldm
drug-discovery,Geometric Latent Diffusion Models for 3D Molecule Generation
User: minkaixu
deep-generative-model diffusion-models drug-discovery geometric-deep-learning icml-2023 molecule molecule-generation

mir-group / allegro
drug-discovery,Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials
Organization: mir-group
Home Page: https://www.nature.com/articles/s41467-023-36329-y
atomistic-simulations computational-chemistry deep-learning drug-discovery force-fields interatomic-potentials machine-learning materials-science molecular-dynamics pytorch

mir-group / nequip
drug-discovery,NequIP is a code for building E(3)-equivariant interatomic potentials
Organization: mir-group
Home Page: https://www.nature.com/articles/s41467-022-29939-5
machine-learning atomistic-simulations molecular-dynamics computational-chemistry deep-learning interatomic-potentials force-fields pytorch drug-discovery materials-science

mobleylab / drug-computing
drug-discovery,Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
Organization: mobleylab
drug-discovery python molecular-dynamics molecular-dynamics-simulation monte-carlo docking ligand-screening solubility teaching-materials educational-software

molecularai / reinvent4
drug-discovery,AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
Organization: molecularai
ai cheminformatics chemistry denovo-design generative-ai ml molecule-generation astrazeneca deep-learning neural-networks

molecularsets / moses
drug-discovery,Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
Organization: molecularsets
Home Page: https://arxiv.org/abs/1811.12823
machine-learning generative-models drug-discovery benchmark

nvidia / deeplearningexamples
drug-discovery,State-of-the-Art Deep Learning scripts organized by models - easy to train and deploy with reproducible accuracy and performance on enterprise-grade infrastructure.
Organization: nvidia
computer-vision deep-learning drug-discovery forecasting large-language-models mxnet paddlepaddle pytorch recommender-systems speech-recognition

octavian-ganea / equidock_public
drug-discovery,EquiDock: geometric deep learning for fast rigid 3D protein-protein docking
User: octavian-ganea
geometry proteins protein-protein-interaction docking graphneuralnetwork deeplearning equivariant-network equivariance equivariant-representations drugdiscovery

pcko1 / deep-drug-coder
drug-discovery,A tensorflow.keras generative neural network for de novo drug design, first-authored in Nature Machine Intelligence while working at AstraZeneca.
User: pcko1
Home Page: https://www.nature.com/articles/s42256-020-0174-5
drug-discovery neural-network denovo-design lstm-neural-networks autoencoders smiles-strings molecules

rdk / p2rank
drug-discovery,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.
User: rdk
Home Page: https://rdk.github.io/p2rank/
bioinformatics machine-learning protein-structure pdb binding-sites proteins ligand protein-surface structural-bioinformatics protein-ligand-interactions

rdkit / rdkit-js
drug-discovery,A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit .
Organization: rdkit
Home Page: https://rdkitjs.com
cheminformatics rdkit javascript wasm react npm node-js molecule molecule-viewer molecule-visualization

shen-lab / deepaffinity
drug-discovery,Protein-compound affinity prediction through unified RNN-CNN
User: shen-lab
drug-discovery interpretable-deep-learning semi-supervised-learning attention-mechanism protein

shenwanxiang / bidd-molmap
drug-discovery,MolMapNet: An Efficient ConvNet with Knowledge-based Molecular Represenations for Molecular Deep Learning
User: shenwanxiang
Home Page: https://molmap.readthedocs.io/en/latest/
deep-learning descriptors drug-discovery fingerprint molecular-represenation molmapnet pharmacophorefp

sustainable-processes / summit
drug-discovery,Optimising chemical reactions using machine learning
Organization: sustainable-processes
Home Page: https://gosummit.readthedocs.io/en/latest/
chemistry machine-learning optimization bayesian-optimization neural-networks drug-discovery tsemo snobfit nelder-mead self-optimization