drug-design

There are 13 repositories under drug-design topic.

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 656
AspirinCode / papers-for-molecular-design-using-DL
List of molecular design using Generative AI and Deep Learning
generative-ai molecular-design deep-generative-models drug-design diffusion gan gnns lstm reinforcement-learning rnn transformer vae energy-based-model prompt-learning score-based-generative-models
507
datamol-io / datamol
Molecular Processing Made Easy.
python molecule rdkit drug-discovery drug-design molecules cheminformatics medicinal-chemistry
Language:Python 422
chemosim-lab / ProLIF
Interaction Fingerprints for protein-ligand complexes and more
molecular-dynamics rdkit drug-design docking cheminformatics mdanalysis
Language:Python 321
arneschneuing / DiffSBDD
A Euclidean diffusion model for structure-based drug design.
ddpm drug-design equivariance generative-model graph-neural-networks machine-learning
Language:Python 286
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 245
igashov / DiffLinker
DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design
diffusion-models drug-design equivariance fragment-based-drug-discovery machine-learning molecular-linker
Language:Python 233
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 205
guanjq / targetdiff
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 iclr2023
Language:Python 173
joofio / py4chemoinformatics
Python for chemoinformatics
chemoinformatics cheminformatics python rdkit jupyter scikit-learn deep-learning chemistry drug-discovery drug-design cv machine-learning
Language:Jupyter Notebook 102
LIYUESEN / druggpt
DrugGPT: A GPT-based Strategy for Designing Potential Ligands Targeting Specific Proteins
drug-design drug-discovery gpt huggingface large-language-models
Language:Python 88
awesome-drug-pair-scoring
AstraZeneca / awesome-drug-pair-scoring
Readings for "A Unified View of Relational Deep Learning for Drug Pair Scoring." (IJCAI 2022)
ddi drug-synergy synergy-prediction deep-chemistry chemistry polypharmacy deep-learning machine-learning relational-learning drug-combination drug-drug-interaction drug-repurposing drug-design drug-target-interactions drug gcn gnn knowledge-graph graph-neural-network decagon
86
futianfan / clinical-trial-outcome-prediction
benchmark dataset and Deep learning method (Hierarchical Interaction Network, HINT) for clinical trial approval probability prediction, published in Cell Patterns 2022.
clinical-trials clinical-data graph-neural-networks benchmark-datasets dataset-generation benchmark drug-design drug-development life-sciences dataset therapeutics clinical-research-data-warehouse clinical-research machine-learning deep-learning
Language:Python 84
awesome-molecular-docking
Thinklab-SJTU / awesome-molecular-docking
We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.
ai-aided-drug-discovery awesome drug-discovery molecular-docking paper-list bioinformatics machine-learning protein-protein-interaction molecular-dynamics binding generative-model drug-design equivariant-representations drug-protein-interactions geometric-deep-learning awesome-list deep-learning optimal-transport protein-ligand-docking drugai
84
asarigun / awesome-denovo-papers
Awesome De novo drugs design papers
cheminformatics deep-generative-models deep-learning denovo-design diffusion-model drug-design drug-discovery gans gcn generative-model gnns machine-learning neural-networks paper target-based-drug variational-autoencoder
73
BALL-Project / ball
The Biochemical Algorithms Library
c-plus-plus structural-biology chemoinformatics force-field computational-biology drug-design
Language:C++ 72
futianfan / reinforced-genetic-algorithm
Structure-based Drug Design; Reinforcement Learning and Genetic Algorithm
drug-design drug-discovery genetic-algorithm molecule-generation reinforcement-learning
Language:Python 57
Networks-Learning / nevae
Code and data for "NeVAE: A Deep Generative Model for Molecular Graphs", AAAI 2019
deep-learning machine-learning drug-discovery drug-design graphs
Language:Python 54
cch1999 / posecheck
Pose checks for 3D Structure-based Drug Design methods
docking drug-design generative-model molecule-generation
Language:Python 53
mims-harvard / TxGNN
TxGNN: Zero-shot prediction of therapeutic use with geometric deep learning and clinician centered design
drug-design drug-discovery geometric-deep-learning graph-neural-networks indications-and-warning knowledge-graph precision-medicine therapeutics
Language:Python 49
lucidrains / neural-plexer-pytorch
Implementation of Nvidia's NeuralPlexer, for end-to-end differentiable design of functional small-molecules and ligand-binding proteins, in Pytorch
artificial-intelligence deep-learning denoising-diffusion drug-design protein-ligand-interactions
Language:Python 48
kotori-y / Scopy
An integrated negative design python library for desirable HTS/VS database design
python rdkit cheminformatics drug-design compounds-filter pypi-package conda-packages drug-discovery
Language:Python 42
biocheming / watvina
implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking
autodock-vina molecular-docking water-docking drug-design watvina pharmacophore
Language:Jupyter Notebook 41
protwis / protwis
Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
bioinformatics cheminformatics chemogenomics drug-design drug-discovery gpcr hacktoberfest open-science pharmacogenomics
Language:Python 33
ram-compbio / CANDO
Computational Analysis of Novel Drug Opportunities
drug-discovery drug-repurposing drug-design multitarget shotgun python bioinformatics biomedical-informatics machine-learning docking
Language:Python 33
chupvl / awesome-ls-ventures
Awesome list of the data and AI/ML related projects with direct Life Science Companies participation
ai biotech drug-design drug-development drug-discovery life-sciences ml pharma
27
rinikerlab / reeds
This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
drug-design free-energy-calculations gromos python hpc replica-exchange enhanced-sampling eds workflow
Language:Python 27
RyanZR / labodock
LABODOCK: A Colab-Based Molecular Docking Tools
autodock-vina cheminformatics drug-design google-colab molecular-docking plip virtual-screening
Language:Jupyter Notebook 27
futianfan / DST
(differentiable) gradient-based optimization on a chemical graph for de novo molecule design/optimization (ICLR 2022)
cheminformatics denovo-design drug-design drug-discovery graph-neural-networks molecule-gene
Language:Python 25
suneelbvs / rdkit_tutorials
rdKit basics (provided jupyter notebooks are custom curated and will help the users to start working on rdKit)
cheminformatics drug-design jupyter-notebook python rdkit rdkit-chem
Language:Jupyter Notebook 25
protwis / gpcrdb_data
This repository is the collection point of reference data for the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
gpcr cheminformatics chemogenomics bioinformatics open-science drug-discovery drug-design pharmacogenomics hacktoberfest
Language:HTML 24
Dunni3 / keypoint-diffusion
A diffusion model for structure-based drug design with faster inference from learned representations of protein structure.
computational-biology diffusion-models drug-design generative-model graph-neural-networks machine-learning
Language:Python 20
CSBG-LSU / BionoiNet
Pytorch implementation of BionoiNet, which is a deep learning-based software to classify ligand-binding sites.
binding-sites convolutional-neural-network deep-neural-network structural-biology drug-design deep-learning
Language:Python 19
gmum / mldd23
The repository for the course "Machine Learning in Drug Design" taught at the Jagiellonian University in 2023. The page is hosted by the machine learning research group GMUM.
cheminformatics computer-aided-drug-design deep-learning drug-design drug-discovery machine-learning pharmacoinformatics
Language:HTML 18
jostorge / diffusion-hopping
DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping
bioinformatics deep-learning drug-design drug-discovery geometric-deep-learning gnn pytorch
Language:Python 18
SENSAAS / sensaas
Shape-based alignment of molecules using 3D point-based representation
bioinformatics chemicals cheminformatics computational-chemistry drug-design molecular-modeling molecules
Language:Python 16