MD Ensemble Generation for Virtual Screening of a Flexible Viral Protein Oligomerization Domain

Dataset accompanying the manuscript "MD Ensemble Generation for Virtual Screening of a Flexible Viral Protein Oligomerization Domain" submitted to Molecular Informatics. This dataset contains all input files, results, and analysis scripts for multi-replica molecular dynamics (MD) ensemble docking of the Nipah virus P protein oligomerization domain (residues 480–595, PDB: 9FUX). Three ff19SB/OPC replicas (50 ns each) with ff14SB/TIP3P cross-validation were performed using AMBER 24. Hierarchical agglomerative clustering yielded 10 representative structures spanning Cα RMSD 7.66–16.02 Å. Virtual screening of 7,662 compounds was conducted with AutoDock Vina 1.2.7 against both MD (10 structures) and NMA (7 structures) ensembles. Contents: (1) AMBER MD input files and topologies, (2) cluster representative structures, (3) BIC-based cluster optimization scripts and results, (4) docking receptor files (PDB/PDBQT), (5) full screening results with ANOVA variance decomposition and robustness classification, (6) analysis scripts (Python/cpptraj), (7) publication figures, (8) compound library (7,662 PDBQT files). Production trajectories (~44 GB total) are available from the corresponding author upon request.