Data and analysis package for: VIBE - Reconstruction of Molecular Assemblies across Periodic Boundaries with Explicit Uncertainty

Abstract

Version 3.1.0 of the data and analysis package supporting VIBE: Reconstruction of Molecular Assemblies across Periodic Boundaries with Explicit Uncertainty. It keeps every file of version 3.0.0 and adds vibe_data_v103_supplement_20260925.zip, in which the VIBE calculations of the article are run with the public release TITAN-VIBE 1.0.3 (https://doi.org/10.5281/zenodo.22955192): the 3,600 generated and 4,320 noisy designed frames, analyzed twice; the development and held-out designed cases; the five molecular systems with the MDVWhole and FixBox comparisons; the local-mode and global-mode check; and the paired time and memory measurements. It also adds a lattice-shift test on three compact assemblies, a retained-contact test, and the 13 range-boundary cases rerun with a wider search range. The supplement holds frame reports, result tables, the protocol amendment and lock, and the driver scripts. Reconstructed coordinate files that are identical to version 3.0.0 are listed with their SHA-256 instead of being copied. Its README maps each folder to the sections of the article. The 11 September archive (vibe_data_update_20260911.zip, 17 parts) includes the extracted frame subsets, topology dependencies, reconstructed outputs, frame and case tables, timing records, environment metadata, original protocols, analysis scripts, generation exclusions, and SHA-256 manifests. See DOWNLOAD_AND_EXTRACT.md to join, verify, and extract it. Complete production trajectories are not included. The software, including the executable used for these calculations, is archived at https://doi.org/10.5281/zenodo.22955192 (MIT License). The previous data version is https://doi.org/10.5281/zenodo.22710653. Funding: Vietnam National Foundation for Science and Technology Development (NAFOSTED), grant 103.01-2025.110.