Supplementary Data for: Transient Aggregation-Prone States in Disordered Proteins as Therapeutic Targets: The Amyloid-β Case

This repository contains the complete computational dataset supporting the manuscript "Transient Aggregation-Prone States in Disordered Proteins as Therapeutic Targets: The Amyloid-β Case". The dataset enables full reproduction of the computational workflow, including Temperature Replica Exchange Molecular Dynamics (T-REMD) simulations, HADDOCK protein-protein docking, and subsequent analysis used to identify and characterize aggregation-prone conformational states of the Aβ42 peptide. Contents 1. structures/- starting_conformations_TREMD/: 72 initial Aβ42 conformations for T-REMD initialization (.gro format)- representative_clusters_TREMD/: Representative cluster structures from T-REMD simulations using OPLS and a99SB-UCB force fields (.xtc format)- aggregation_prone_conformations/: Aβ42 monomers classified as aggregation-prone (.pdb format)- non_aggregation_prone_conformations/: Aβ42 monomers classified as non-aggregation-prone (.pdb format) 2. parameters/- mdp_files_TREMD/: GROMACS molecular dynamics parameter files and generation scripts for all 72 T-REMD replicas- HADDOCK_homodimer_docking/: Complete HADDOCK 2.4 input files for Aβ-Aβ homodimer docking- HADDOCK_DNAJB6_docking/: Complete HADDOCK 2.4 input files for Aβ-DNAJB6 docking validation 3. processed_data/- correlation_homodimer_docking/: Correlation analysis between HADDOCK scores and structural descriptors for different time windows (600-800 ns and 800-1000 ns)- correlation_DNAJB6/: Correlation analysis between Aβ-Aβ and Aβ-DNAJB6 HADDOCK scores 4. analysis_scripts/- clustering_analysis.sh: GROMOS clustering of MD trajectories- calculate_chemical_shifts.tcl: VMD/SPARTA+ script for NMR chemical shift calculations- calculate_jcoupling.tcl: VMD script for ³JHNHα coupling constant calculations- pearson_correlation_descriptors.py: Correlation analysis between HADDOCK scores and structural descriptors- pearson_correlation_dnajb6.py: Analysis of Aβ-Aβ vs Aβ-DNAJB6 binding correlation Software Requirements - GROMACS 2022.4 (or compatible)- HADDOCK 2.4- VMD 1.9.3 (or compatible)- SPARTA+ 2.88 (or later)- Python 3 with standard scientific libraries Usage Complete documentation, including detailed usage instructions for all scripts and reproduction protocols, is provided in the README.md file included in this repository. Contact For questions regarding this dataset, please contact: [e-mail], [e-mail]