Data for "How Natural Sequence Variation Modulates Protein Folding Dynamics"

Description

This repository contains the data associated with the article:"How Natural Sequence Variation Modulates Protein Folding Dynamics"Authors: Ezequiel A. Galpern, Ernesto A. Roman, Diego U. FerreiroDOI: 10.48550/arXiv.2412.14341

The dataset includes:

Multiple Sequence Alignments (MSAs): Provided as .fasta files for 15 protein families.

Potts Models: Saved as Python dictionaries in .npz format, which include:

h: Local fields of the Potts model.

J: Couplings of the Potts model.

This dataset is designed to support reproducibility and further exploration of the findings presented in the article.

Data Structure

/simplified_rbm_and_msa/: Contains a folder for each of the 15 protein families. Each folder includes:

A .fasta file for the multiple sequence alignment (MSA) of the protein family.

A  .npz file containing the Potts model, with local fields (h) and couplings (J), saved in NumPy format.

File Format Details

MSA Files

Format: .fasta

Example Usage: Load using any standard MSA tool or Python libraries such as Biopython.

Potts Model Files

Format: .npz (NumPy compressed archive)

Contents:

h: Local fields, accessible as potts['h'].

J: Couplings, accessible as potts['J'].

Example Usage:

import numpy as np

potts = np.load("potts_file.npz")

h = potts['h'] # Local fields

J = potts['J'] # Couplings

Usage Instructions

To use this dataset, refer to the corresponding GitHub repository, which includes:

Codebase: All scripts required to process and analyze the data.

Demonstration Notebook: A ready-to-run Jupyter Notebook for Google Colab.

GitHub Repository

Access the repository here: github.com/eagalpern/folding-ising-globular

Citing This Dataset

If you use this dataset, please cite:

Galpern, E. A., Roman, E. A., & Ferreiro, D. U. (2024). "How Natural Sequence Variation Modulates Protein Folding Dynamics". arXiv. DOI: 10.48550/arXiv.2412.14341.