Data for "Inferring protein folding mechanisms from natural sequence diversity"

Description This repository contains the data associated with the article:"Inferring protein folding mechanisms from natural sequence diversity"Authors: Ezequiel A. Galpern, Ernesto A. Roman, Diego U. FerreiroDOI: 10.1016/j.bpj.2025.06.034 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. (2025). "Inferring protein folding mechanisms from natural sequence diversity". Biophysical Journal . DOI: 10.1016/j.bpj.2025.06.034 .