MSAffect

Aarav H. Dave¹

Summary

This repository implements MSAffect, a computational pipeline for generating, perturbing, and analyzing multiple-sequence alignments (MSAs) in the context of protein structure prediction with AlphaFold2. It automates:

• Baseline MSA generation via ColabFold/MMseqs2
• Three adversarial perturbations (deletion, residue-level mutation, row-and-column shuffle)
• AlphaFold2 runs on both unperturbed and perturbed MSAs
• Extraction of confidence scores (pLDDT) and structural deviation metrics (RMSD)
• Generation of summary tables, bar plots, scatterplots, and 3D visualizations

This repository hosts project files (2025.1α) for public usage dictated by its license.

Abstract

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Paper

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Installation

1. Open MSAffect.ipynb in a Google Colaboratory environment.
2. Install dependencies by running “Initiate MSAffect Environment” cell, which will install ColabFold, Biopython, NumPy, Matplotlib, and py3Dmol.
3. Prepare your FASTA inputs by placing one or more .fasta files in the msa/ directory. ubiquitin.fasta, bpti.fasta, and calmodulin.fasta are included as examples.
4. Execute the pipeline by running the “Run MSAffect” cell. The script will process every FASTA in msa/, create subfolders under results/, and produce summary tables and figures. You can visualize your results in 3D by running the "3D Visualize Results" cell.
5. Contribute edits by adding your GitHub token and running the "Push to MSAffect GitHub" cell.

Recognitions

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Technical Specifications

This software utilizes:

• Google Colaboratory for interactive execution and free GPU access
• ColabFold (AlphaFold2) for accelerated MSA generation and structure prediction
• Python 3.11 as the execution environment
• Biopython for MSA parsing and PDB handling
• NumPy for numerical operations
• Matplotlib (and optional Seaborn) for plotting
• py3Dmol for in-notebook 3D molecular visualization

License

This software, as with all subsequent versions of the software, is protected by the CC-BY-NC-ND license. In summary, this does not allow commercial usage, distribution, or distribution of modifications of the software. In additon, you are required to credit authorship and state any changes you may have made.

For more information, please refer to the LICENSE file.

Contacts

For questions concerning the contents of this repository, please contact contact [at] aaravdave [dot] org.

Footnotes

1. Lowndes High School, Valdosta, GA ↩