alpharing 2.0.0

Interpretable, protein structure-based prediction of missense variant deleteriousness

AlphaRING v2 (AlphaRING-X)

AlphaRING is a package designed for interpretable, protein structure-based prediction of missense variant deleteriousness.

To predict the deleteriousness of a missense variant, AlphaRING performs the following steps:

1. Predicts the structure of the wild-type protein using AlphaFold to extract the pLDDT of the substituted wild-type residue.
2. Converts wild-type structure into a residue interaction network using RING to extract the degree of the substituted wild-type residue.
3. Uses wild-type structure to calculate the ΔΔG of the substitution using FoldX and extracts it.
4. Calculates the relative substitution position (RSP) along the protein.
5. Feeds pLDDT, degree, ΔΔG, and RSP into an in-house XGBoost classifier trained to classify missense variant deleteriousness.
6. Outputs the probability of deleteriousness and feature SHAP values to explain the prediction mechanistically.

[!NOTE] AlphaRING-X manuscript and benchmarking data/scripts (including for classifier training/calibrating/testing) will be released soon.

Installation

Before installation, ensure you have a Linux machine equipped with a modern NVIDIA GPU and the following:

1. Full AlphaFold v2 genetic database
2. RING v4
3. FoldX v5.1
4. Miniconda

To install AlphaRING, please do the following:

1. Create an environment for AlphaRING using Miniconda:

   conda create -n alpharing -c bioconda -c conda-forge python==3.10 hmmer kalign2 pdbfixer hhsuite==3.3.0 openmm==8.0.0
   

2. Activate the environment and install AlphaRING:

   conda activate alpharing
   pip install alpharing
   

Usage

To predict the deleteriousness of a missense variant, activate the AlphaRING environment and execute the alpharing command as follows:

alpharing \
  --fasta_path=... \
  --substitutions=... \
  --output_dir=... \
  --data_dir=... \
  --ring_exe_path=... \
  --foldx_exe_path=...

Argument breakdown:

• --fasta_path: path to a FASTA file representing the wild-type protein. See here for an example.
• --substitutions: list of one or more single-residue substitutions to be individually applied to the wild-type protein. Please represent the substitutions in FoldX format, e.g., WA70Y, where W is the wild-type residue, A is the chain, 70 is the substitution position, and Y is the variant residue. For AlphaRING, the chain should always be A. If multiple substitutions are provided, please separate them with commas only, e.g., WA70Y,WA80F.
• --output_dir: path to the directory that will store the output.
• --data_dir: path to the directory of the full AlphaFold database.
• --ring_exe_path: path to the RING executable. This should remain in the original installation.
• --foldx_exe_path: path to the FoldX executable. This should remain in the original installation.

Downstream

AlphaRING stores the output in a subdirectory within the directory specified by --output_dir. The subdirectory is named after the basename of the FASTA file specified by --fasta_path. In addition to the default AlphaFold, RING, and FoldX outputs, the subdirectory contains the file alpharing_scores.txt, which summarises the feature values, deleteriousness probability, and feature SHAP values of each substitution specified by --substitutions.

[!NOTE] For efficiency, when running a prediction, AlphaRING will check if the FASTA file specified by --fasta_path already has its corresponding output subdirectory with an AlphaFold relaxed model file, and, if found, will skip running AlphaFold.