Open Source Malaria Series 4 Manuscript

This repository contains executable notebooks and links related to the OSM Series 4 work by Ersilia.

The manuscript

The current manuscript is publicly visible in this online document. We expect to submit it as a Note to ACS Medicinal Chemistry Letters in response to this call for papers related to AI.

Author guidelines

Author guidelines can be found here and a short comment on how to increase chances of acceptance can be found here.

In sum:

• Abstract: 150 words.
• Text: 2500 words, no sections.
• References: 30.
• Figures and tables: 2-4.
• Figures format: One column: up to 240 pt (3.33 in). Two columns: between 300 and 504 pt (4.167 in. and 7 in.). Lettering no smaller than 4.5 pt.

Resources

• OSM Issue #34
• Generative modelling, round 1
• Generative modelling, round 2
• Predictive model
• Selection of candidates for synthesis
• PfATP4 AlphaFold Structure
• ChemSampler

Installation

Create a conda environment and activate it.

conda create -n osms4 python=3.11
conda activate osms4

Install Ersilia Compound Embeddings and after you have installed it.

cd ~/Desktop
git clone https://github.com/ersilia-os/compound-embedding.git
cd compound-embedding/lite
pip install .
cd ../..
rm -r compound-embedding

Install other necessary Python libraries.

pip install pandas
pip install umap-learn
pip install statsmodels
pip install git+https://github.com/ersilia-os/stylia.git

Usage

In the notebooks folder, there are two Juypter Notebooks that are used to produce the display items of the manuscript.

• ChemicalSpaceExploration.ipynb is used for the main Figure 1.
• CompetitionBenchmark.ipynb is used for the supplementary Figure S1.