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Top 28 drug-discovery open source projects

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

✭ 3,324

python Jupyter Notebook hacktoberfest deep-learning biology quantum-chemistry drug-discovery materials-science

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

✭ 38

C++perl matlab Meson python Rich Text Format protein-ligand-docking drug-discovery docking ligand-screening protein-ligand-interactions virtual-screening cxx11 protein-ligand-binding-conformation protein-ligand-interfaces molecular-docking protein-drug-interactions

FMol

A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.

✭ 13

python matlab shell Makefile protein drug-discovery alphafold fpocket

chemicalx

A PyTorch and TorchDrug based deep learning library for drug pair scoring.

Rcpi

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

✭ 22

r bioinformatics cheminformatics fingerprint feature-extraction bioconductor drug-discovery protein-sequences molecular-descriptors

AMIDD

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

✭ 13

TeX CSS bioinformatics statistics teaching drug-discovery informatics applied-mathematics chemoinformatics computing

Calibrated-Boosting-Forest

Original implementation of Calibrated Boosting-Forest

✭ 18

python shell machine-learning xgboost drug-discovery

cbh21-protein-solubility-challenge

Template with code & dataset for the "Structural basis for solubility in protein expression systems" challenge at the Copenhagen Bioinformatics Hackathon 2021.

✭ 15

python Dockerfile hackathon protein-structure protein drug-discovery solubility-prediction

awesome-small-molecule-ml

A curated list of resources for machine learning for small-molecule drug discovery

✭ 54

machine-learning awesome bioinformatics cheminformatics drug-discovery awesome-list

skywalkR

code for Gogleva et al manuscript

✭ 28

r ui knowledge-graph drug-discovery recommender-system shiny-apps

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).

✭ 20

python javascript HTML CSS bioinformatics cheminformatics open-science drug-discovery drug-design hacktoberfest pharmacogenomics chemogenomics gpcr

CANDO

Computational Analysis of Novel Drug Opportunities

✭ 27

python Jupyter Notebook machine-learning bioinformatics shotgun biomedical-informatics drug-discovery drug-repurposing docking drug-design multitarget

PyPLIF-HIPPOS

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS

✭ 15

python shell drug-discovery virtual-screening molecular-docking autodock-vina interaction-fingerprinting

egfr-att

Drug effect prediction using neural network

✭ 17

python Jupyter Notebook cnn classification drug-discovery attention-mechanism egfr

paccmann rl

Code pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6

✭ 22

deep-learning drug-discovery transcriptomics generative-models drug-sensitivity de-novo-drug-design

Scopy

An integrated negative design python library for desirable HTS/VS database design

✭ 28

python java cheminformatics drug-discovery rdkit drug-design conda-packages pypi-package compounds-filter

Deep-Drug-Coder

A tensorflow.keras generative neural network for de novo drug design, first-authored in Nature Machine Intelligence while working at AstraZeneca.

✭ 143

python Jupyter Notebook neural-network drug-discovery molecules autoencoders lstm-neural-networks denovo-design smiles-strings

screenlamp

screenlamp is a Python toolkit for hypothesis-driven virtual screening

✭ 20

python bioinformatics computational-biology computational-chemistry drug-discovery docking pharmacometrics ligand-screening virtual-screening

GLaDOS

Web Interface for ChEMBL @ EMBL-EBI

✭ 28

javascript coffeescript python HTML CSS shell chemistry cheminformatics molecular-structures webapp drug-discovery chemoinformatics chembl drug-targets

py4chemoinformatics

Python for chemoinformatics

✭ 78

machine-learning deep-learning jupyter chemistry cheminformatics scikit-learn cv drug-discovery rdkit chemoinformatics drug-design

bidd-molmap

MolMap: An Efficient Convolutional Neural Network Based Molecular Deep Learning Tool

✭ 102

HTML Jupyter Notebook python deep-learning fingerprint drug-discovery descriptors molmapnet pharmacophorefp

NDD

Drug-Drug Interaction Predicting by Neural Network Using Integrated Similarity

✭ 25

python deep-neural-networks neural-network similarity neural-networks drug-discovery similarity-measures predictive-modeling snf ndd drug-drug-interaction drug-target-interactions drug-similarities

chemprop

Fast and scalable uncertainty quantification for neural molecular property prediction, accelerated optimization, and guided virtual screening.

✭ 75

python HTML CSS shell neural-network chemistry molecule uncertainty drug-discovery bayesian-optimization active-learning virtual-screening evidential-deep-learning

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.

✭ 179

Jupyter Notebook cheminformatics protein-structure jupyter-notebook computational-biology protein drug-discovery drug-repurposing rdkit openbabel drug-design mdanalysis autodock ledock molecular-docking autodock-vina py3dmol

nequip

NequIP is a code for building E(3)-equivariant interatomic potentials

✭ 312

python machine-learning deep-learning molecular-dynamics pytorch computational-chemistry drug-discovery materials-science atomistic-simulations force-fields interatomic-potentials

MolDQN-pytorch

A PyTorch Implementation of "Optimization of Molecules via Deep Reinforcement Learning".

✭ 58

python machine-learning reinforcement-learning deep-learning chemistry molecule pytorch drug-discovery materials-science materials-informatics pytorch-rl pytorch-implementation dqn-pytorch inverse-design

pinot

Probabilistic Inference for NOvel Therapeutics

✭ 15

python TeX shell drug-discovery

graph-neural-networks-for-drug-discovery

odr.chalmers.se/handle/20.500.12380/256629?locale=en

✭ 78

python deep-learning pytorch drug-discovery graph-neural-networks astrazeneca

1-28 of 28 drug-discovery projects