Structural and thermodynamic landscape of the HPV E1–E2 recruitment interface across high-risk and low-risk genotypes

This repository contains the structural models, sequence alignments, and computational scripts used to support the conclusions of the manuscript "Thermodynamic plasticity of the HPV E1-E2 recruitment interface differentiates high-risk and low-risk genotypes". The overarching purpose of this data package is to ensure full methodological transparency and to allow other researchers to replicate our evolutionary, structural, and thermodynamic analyses. Repository Contents: Commands.txt: A compiled text document containing all the command-line instructions and Python scripts used throughout the workflow. This includes the MAFFT alignment commands, PyMOL trimming steps, FoldX and PRODIGY automation scripts, and the logistic regression code. MSA Files.zip: The MAFFT aligned FASTA files for the HPV E1 proteins across the evaluated genera. GUIDANCE2 Scores.zip: The confidence scoring outputs generated by GUIDANCE2 used to validate the reliability of our multiple sequence alignments. HPV Types Analyzed.csv: A reference list of the 194 specific HPV genotypes utilized in the alignment phases of the study. AF3 E1-E2 CIF Files.zip: The 24 raw AlphaFold3 structural models for the E1-E2 heterodimeric regulatory complexes. AF3 E1-E1 CIF Files.zip: The 24 raw AlphaFold3 structural models for the E1-E1 hexameric helicase assemblies. Supplementary_Materials.pdf: Additional data tables, comprehensive geometric analyses, and detailed conservation scoring profiles referenced in the main text of the manuscript.