ProteusAI

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ProteusAI is a library for the machine learning driven engineering of proteins. The library enables workflows from protein structure prediction, prediction of mutational effects to protein ligand interactions powered by artificial intelligence.

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![App_Overview](https://github.com/user-attachments/assets/6a11e863-a45e-47d3-903d-8fb5bc260cd2)

# ProteusAI
ProteusAI is a library for machine learning-guided protein design and engineering. 
The library enables workflows from protein structure prediction, the prediction of 
mutational effects-, and zero-shot prediction of mutational effects.
The goal is to provide state-of-the-art machine learning for protein engineering in a central library.

ProteusAI is primarily powered by [PyTorch](https://pytorch.org/get-started/locally/), 
[scikit-learn](https://scikit-learn.org/stable/), 
and [ESM](https://github.com/facebookresearch/esm) protein language models.

Cite our preprint [here](https://www.biorxiv.org/content/10.1101/2024.10.01.616114v1).

Test out the ProteusAI web app [proteusai.bio](http://proteusai.bio/)

## Getting started

----
The commands used below are tested on Ubuntu 20.04 and IOS. Some tweaks may be needed for other OS.
We recommend using conda environments to install ProteusAI.

Clone the repository and cd to ProteusAI:
```bash
git clone https://github.com/jonfunk21/ProteusAI.git
cd ProteusAI 
```

Install the latest version of proteusAI in a new environment
```bash
conda env create -n proteusAI
conda activate proteusAI
```

This uses the `environment.yml` file to install the dependencies.

## GPU support
By default proteus will install torch-scatter using cpu compatible binaries.
If you want to take full advantage of GPUs for the Design module consider
uninstalling the default `torch-scatter`, and replace it with the CUDA 
compatible version:

```bash
pip uninstall torch-scatter
pip install torch-scatter -f https://data.pyg.org/whl/torch-${TORCH_VERSION}+cuda.html
```

If you have acces to GPUs you can run ESM-Fold. Unfortunately the installation of 
openfold can be unstable for some people. Please follow installation instructions
on of the [ESM repository](https://github.com/facebookresearch/esm) and use 
the discussions in the issues section for help.

### Install using pip locally for developement

Install a local version which picks up the latest changes using an editable install:

```bash
# conda env create -n proteusAI python=3.8
# conda activate proteusAI
pip install -e . --find-links https://data.pyg.org/whl/torch-2.4.1+cpu.html
```

### Troubleshooting
You can check a working configuration for a Ubuntu machine (VM) 
in the `proteusEnvironment.yml` file. The latest versions can be checked by us via
our actions.

### Setting shiny server

Install Shiny Server on Ubuntu 18.04+ (the instructions for other systems are availabe at <a href="https://posit.co/download/shiny-server/?_gl=1*1mdig69*_ga*MTQ1ODYyNTEzMC4xNzE5ODQwMDQy*_ga_8QJS108GF1*MTcxOTg0Mzg4MC4yLjEuMTcxOTg0Mzg4My4wLjAuMA..*_ga_2C0WZ1JHG0*MTcxOTg0Mzg4MC4yLjEuMTcxOTg0Mzg4My4wLjAuMA.." target="_blank">posit.co</a>, please skip the section about R Shiny packages installation) with the following commands:
```bash
sudo apt-get install gdebi-core
wget https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-1.5.22.1017-amd64.deb
sudo gdebi shiny-server-1.5.22.1017-amd64.deb
```

Edit the default config file `/etc/shiny-server/shiny-server.conf` for Shiny Server (the `sudo` command or root privileges are required):
```bash
# Use python from the virtual environment to run Shiny apps
python /home/proteus_developer/miniforge3/envs/proteusAI_depl/bin/python;

# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;

# Never delete logs regardless of the their exit code
preserve_logs true;

# Do not replace errors with the generic error message, show them as they are
sanitize_errors false;

# Define a server that listens on port 80
server {
  listen 80;

# Define a location at the base URL
  location / {

# Host the directory of Shiny Apps stored in this directory
    site_dir /srv/shiny-server;

# Log all Shiny output to files in this directory
    log_dir /var/log/shiny-server;

# When a user visits the base URL rather than a particular application,
    # an index of the applications available in this directory will be shown.
    directory_index on;
  }
}
```
Restart the shiny server with the following command to apply the server configuration changes:
```bash
sudo systemctl restart shiny-server
```
If you deploy the app on your local machine, be sure that the port 80 is open and not blocked by a firewall. You can check it with `netstat`:
```bash
nc <your-ip-address> 80
```
If you deploy the app on your Azure Virtual Machine (VM), please add an Inbound Port rule in the <i>Networking - Network Settings</i> section on Azure Portal. Set the following properties:
```yaml
Source: Any
Source port ranges: *
Destination: Any
Service: HTTP
Destination port ranges: 80
Protocol: TCP
Action: Allow
```
Other fields can beleaft as they are by default.

Finally, create symlinks to your app files in the default Shiny Server folder `/srv/shiny-server/`:

```bash
sudo ln -s /home/proteus_developer/ProteusAI/app/app.py /srv/shiny-server/app.py
sudo ln -s /home/proteus_developer/ProteusAI/app/logo.png /srv/shiny-server/logo.png
```
If everything has been done correctly, you must see the application index page available at `http://127.0.0.1` (if you deploy your app locally) or at `http://<insert-your-public-VM-IP-address-here>` (if you deploy your app on an Azure VM). Additionally, the remote app can still be available in your local browser (the Shiny extension in Visual Studio must be enabled) if you run the following terminal command on the VM:
```bash
/home/proteus_developer/miniforge3/envs/proteusAI_depl/bin/python -m shiny run --port 33015 --reload --autoreload-port 43613 /home/proteus_developer/ProteusAI/app/app.py
```
If you get warnings, debug or "Disconnected from the server" messages, it is likely due to: 
- absent python modules,
- updated versions of the current python modules, 
- using relative paths instead of absolute paths (Shiny Server sees relative paths as starting from `/srv/shiny-server/` folder) 
or 
- logical errors in the code.

In order to debug the application, see what is written in the server logs under `/var/log/shiny-server` (the log_dir parameter can be reset in the Shiny Server instance config file `/etc/shiny-server/shiny-server.conf`).

### Note on permissions:
The app may give some problems due to directories not having permissions to create directories or load files to certain directories. When this happen, a solution found was to use  the following:

```bash
chmod 777 directory_name
```

ProteusAI

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