ADME@NCATS

This repository contains the code for the application ADME@NCATS which hosts QSAR models for different ADME endpoints. To use the application locally, you can either use Git to clone the respository, or you can simply download a ZIP file (by clicking the green "Code" button on the top right corner) and then unzip it. The next steps are described below.

If you use Git to clone this repository, please use the --recursive flag:

git clone --recursive https://github.com/ncats/ncats-adme.git

If you download the application, you also need to download and unzip chemprop, but make sure to unzip the contents of chemprop inside the server folder so the the ncats-adme folder/file structure looks something like this:

• ncats-adme
  • client
  • server
    • chemprop
      • chemprop
      • docs
      • scripts
      • ...

Models will be loaded from NCATS servers so you will need access to the internet when you first run the application. Alternatively, if you want to download the models, the files are available as follows:

• Human Liver Microsomal Stability
• Rat Liver Microsomal Stability
• PAMPA 7.4 Permeability
• PAMPA 5.0 Permeability
• PAMPA-BBB Permeability
• Solubility
• Human Liver Cytosol Stability
• CYP450 isozymes - CYP2C9, CYP2D6, CYP3A4

Installing required software

1. Install anaconda or miniconda

Python is also required but it is included with either installation of conda or miniconda.

Setting up the environment

You only have complete these steps one time.

1. Open your terminal

• If you're on Windows, open Anaconda Prompt (window -> Anaconda3 -> Anaconda Prompt)
• If you're on Mac or Linux, open your Terminal

2. Change the working directory (windows or Mac and Linux) to where you have ncats-adme and then go (CD one more time) into the server directory
3. Create environment

• For Windows and Linux machines
  1. Type conda env create --prefix ./env -f environment.yml and hit Enter
  2. Wait several minutes for the envitonment to be created
  3. For Windows machines only, type pip install typed-argument-parser and hit Enter
• For Mac machines
  1. Type conda env create --prefix ./env -f environment_mac.yml and hit Enter
  2. Wait several minutes for the envitonment to be created

Running the application

1. If you're doing this immediately after completing the steps above, skip to step 4
2. Open your terminal

• If you're on Windows, open Anaconda Prompt (window -> Anaconda3 -> Anaconda Prompt)
• If you're on Mac or Linux, open your terminal

3. Change the working directory (windows or Mac and Linux) to where you have ADME_RLM and then go into the server directory
4. Type conda activate ./env and hit Enter
5. Type python app.py and hit Enter
6. Open Chrome or Firefox and browse to http://127.0.0.1:5000/
7. To close the application, hit Ctrl + c or Cmd + c in the Terminal and then type conda deactivate and hit Enter to close the conda environment