Thermodynamic variations at the HPV E1-E2 interface correlate with clinical risk groups: An in-silico analysis

This repository contains the structural models, sequence alignments, and computational scripts used to support the conclusions of the manuscript "Thermodynamic variations at the HPV E1-E2 interface correlate with clinical risk groups: An in-silico analysis". 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 Directory Structure & Contents: 01_sequence_alignment/: Curated multiple sequence alignments of E1 proteins across Alpha, Beta, and Gamma genera, post-alignment GUIDANCE2 column-reliability scores, and PaVE accession mapping table. 02_structural_models/: AlphaFold3-generated three-dimensional structures of E1-E2 complex ensembles and processive hexamers (24 coordinate files), along with PyMOL low-confidence residue trimming scripts. 03_foldx_analysis/: high-throughput Python scripts to automate structural repairs, complex binding energy simulations, and residue-level thermodynamic decompositions using FoldX 5.1. 04_statistical_analysis/: Scientific validation code performing leave-one-out cross-validation (LOOCV), repeated 5-fold cross-validation, permutation tests, outlier sensitivity testing, and phylogenetic regressions. 05_supplementary_results/: Master workbook Supplementary_Tables.xlsx containing all supplementary tables and figures mapped during the peer-review revisions (seed-level raw results, pH 6.5 controls, per-residue thermodynamic matrices, logistic regression outputs, and HPV16 sublineage variations).