ersilia-os/anpdb-annotation

Annotation of the African Natural Products Database using the Ersilia Model Hub, with UB-CeDD. # African Natural Products Database Annotation Pipeline Annotation of ANPDB compounds using the Ersilia Model Hub. This project is part of an ongoing collaboration between Prof. Ntie-Kang's Centre for Drug Discovery at the University of Buea (UB-CeDD) and the Ersilia Open Source Initiative. The purpose of this pipeline is to **annotate the ANPDB** with a few **selected models from the Ersilia Model Hub**. The pipeline starts with chemical structures (SMILES strings) and it returns a table with multiple calculations properties and predictions. At a high level, we calculate the following properties: * Physicochemical properties * Synthetic accessibility properties * ADMET properties * Bioactivity prediction against some pathogens such as _Plasmodium falciparum_ and _Mycobacterium tuberculosis_. * Chemical space exploration components for 2D visualization There is an **app associated with this pipeline**. Click the link below to access it: * ANPDB Annotation Demo App ## Installation We recommend that you create a Conda environment to run the pipeline. A few dependencies are also necessary, such as `rdkit` and the `standardiser`. ```bash conda create -n anpdb-annotation python=3.10 conda activate anpdb-annotation cd anpdb-annotation pip install -r requirements.txt ``` Then you need to make sure that the Ersilia CLI is appropriately installed. Docker should be active in your system. Fetch the following models: ```bash ersilia fetch ``` ## How to run the the pipeline To annotate ANPDB, simply run the following: ```bash bash run_pipeline.sh ``` An `anpdb_annotated.tsv` file will be stored in the `results/` folder. ## How to interpret the results table