Discover ersilia-os/h3d-screening-cascade-code Open Source project

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Created almost 2 years ago
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Code for the manuscript entitled "First fully automated AI/ML virtual screening cascade implemented at a drug discovery centre in Africa"

ersilia

The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.

Python

198

chempfn

Ensemble-based, size-agnostic wrapper for the TabPFN classifier

Jupyter Notebook

zaira-chem

Automated QSAR based on multiple small molecule descriptors

Python

chem-sampler

Sample small molecules, both from large chemical libraries and generated

Python

chemxor

Privacy preserving machine learning for small molecule data

Python

eos2v11

ADMETlab 2 for systematic evaluation of ADMET properties

Python

event-fund-ai-drug-discovery

Coding and data materials for the Event Fund AI for Drug Discovery Course

Jupyter Notebook

compound-embedding

Compound embedding obtained with few-shot learning (FS-Mol), Morgan fingerprints, Grover embeddings, and Mordred descriptors

Jupyter Notebook

olinda

Chemistry model distillation, based on 1024-dimensional embeddings

Python

osm-series4-candidates

New candidates for the Open Source Malaria series 4 compounds

Python

eos7w6n

Grover embedding for molecular representation

Python

eos8a4x

RDKIT physicochemical descriptors of small molecules

Python

eos7asg

PADEL physicochemical descriptors

Python

eos78ao

Mordred physicochemical descriptors

Python

osa-murd

Open Source Antibiotics MurD ligands based on generative models.

Jupyter Notebook

eos1af5

Explainable AI for Caco-2 cell wall permeability

Jupyter Notebook

pharmacogx-embeddings

Pharmacogenomics knowledge graph embeddings and related analyses

Jupyter Notebook

eos5axz

Morgan count fingerprints with radius 3

Python

eos7cpf

Predicts the Lipophilicity (octanol/water distribution coefficient) of small molecules

Python

python101

Materials for the Python Introductory Course

Jupyter Notebook

eos7pw8

Python

eos9ei3

Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions

Python

eos3ae6

Holistic molecular descriptors for scaffold hopping

Python

eos3ae7

Chemical Variational Autoencoder (VAE)

Python

osm-series4-candidates-2

A new round of series 4 candidates, including new low-data generative models and improved predictors

Python

cidrz-e2e-linkage

A fully automated pipeline for fuzzy matching of medical datasets.

Python

eos481p

grover-toxcast

Python

eos2re5

A platform for systematic ADME evaluation of drug molecules

Python

eos2ta5

Ligand-based prediction of hERG blockade

Python

stylia

Decent scientific plot styles

Jupyter Notebook

eos1amr

Predictor of blood-brain-barrier permeability

Python

eos54ij

Cardiac Toxicity Prediction

Python

eos1579

Classification of carcinogenic metabolites

Python

eos5smc

grover-tox21

Python

eos2lm8

SMILES transformer embeddings

Python

griddify

Griddify high-dimensional tabular data for easy visualization and deep learning

Jupyter Notebook

antimicrobial-ml-tasks

Antimicrobial activity prediction with automated machine learning

Jupyter Notebook

model-inference-pipeline

Ersilia's batch inference pipeline on the AWS cloud

Jupyter Notebook

eos43at

Explainable AI applied to hERG blockade

Python

eos1xje

Python

open-data-cleaning

Repository with notebooks that clean open data files downloaded from different sources

Jupyter Notebook

eos6ao8

Explainable AI for plasma protein binding prediction

Jupyter Notebook

lazy-qsar

A library to build fast QSAR models

Python

eos8lok

Python

isaura

A lake of precalculated properties of biomedical entities based on the Ersilia Model Hub

eos2mrz

PyBioMed

groverfeat

An interface to the GROVER model for molecule featurization

Python

eos8ioa

A simple natural product likeness score

Python

eos92sw

Predicts the toxicity and synthetic availability of small molecules

Python

eos2b6f

Jupyter Notebook

eos-template

Template repository to add new models to the Ersilia Model Hub

eos8bhe

eos7ack

chemical-library-exploration

This simple repository performs a fast exploration of a chemical library

Python

osm-series4-synthesis-round1

Selection of candidates for first round of experimental synthesis

HTML

bioassay-db

Scripts to download data from ChEMBL

Python

ersilia-book

Ersilia Book repository

eos8451

grover-esol

Python

eos4u6p

Chemical Checker 25 bioactivity signatures

Python

easylinkage

Standard and extended record linkage functionalities

Python

eos2r5a

Retrosynthetic accessibility score

Python

zaira-chem-tdc

This repository contains the benchmarking of ZairaChem using the Therapeutics Data Commons Datasets

Jupyter Notebook

eos31ve

Python

mock-website

SCSS

eos69p9

Chemical toxicity prediction based on SSL-GCN

Python

eos238c

mesh-therapeutic-use

Python

eos7a04

Continuous and data driven descriptors

Python

auto-tabnet

TabNet implementation with hyperparameter search

Python

autocat-chem

Automatic training of (multioutput) regression models for chemistry

Python

eos8d8a

Mycobacterium tuberculosis membrane permeability of drugs

Perl

eos526j

A tool for planning retrosynthesis of a target molecule based on template reactions and a stock of precursors

Python

pharmacogx-arsa

Look for abundant region specific alleles for pharmacogenomics

Jupyter Notebook

pabb-docking

Docking experiments for the pabb protein

eos157v

eos6fza

fps-grid

Converts molecular fingerprints to grids for image-based DL

Jupyter Notebook

eos7jio

RDKIT path-based fingerprints

Python

eos2thm

MolBERT molecular representation

Python

eos9be7

Frechet Chemnet Distance

Python

osm-pfatp4-structure

Jupyter Notebook

eos6oli

Aqueous solubility prediction

Python

eos93ox

Classification of hERG blockers and nonblockers

Python

eos2fy6

Python

eos4cxk

Python

eos3d3r

CardPred hERG blockade

eos8h6g

eos30gr

eos2lqb

eos77w8

Predicts side-effects of small molecule drugs

Python

ai2050-h3d-symposium-workshop

Material for a 2h introductory workshop on AI/ML for drug discovery

Jupyter Notebook

ersilia-os/h3d-screening-cascade-code

ersilia-os

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