Reproducibility Archive for a Sequence-Aware Workflow for Diagnosing Unresolved-Residue Topology Artifacts in Protein Molecular Dynamics: PCSK9 Case Study

This repository provides the supplementary information and reproducibility archive supporting the manuscript “Thermodynamically plausible but structurally invalid: a sequence-aware workflow for diagnosing unresolved-residue topology artifacts in protein molecular dynamics: PCSK9 as a reproducibility case study.” The archive documents the diagnosis and correction of a structurally invalid apo-PCSK9 molecular-dynamics preparation derived from PDB 3BPS. It contains evidence associated with the original rejected simulation, sequence and unresolved-residue auditing, topology diagnostics, conservative reconstruction of PCSK9 residues 153–446, corrected topology generation, minimization, equilibration, qualification-scale molecular dynamics, and structural analyses. The repository intentionally preserves both failed and corrected computational outputs because the failed trajectory-processing attempts and topology warnings constitute part of the methodological evidence. The corrected 1 ns simulation is provided as a qualification-scale structural-consistency test and is not intended to establish long-timescale PCSK9 conformational stability. Software and principal methods include GROMACS 2023.3, AMBER99SB-ILDN, TIP3P water, UniProt Q8NBP7 sequence verification, and SWISS-MODEL comparative modelling.