2026-10-13T18:54:46Z https://www.scidb.cn/oai

10.57760/sciencedb.45988 2026-08-12T09:40:04Z

2026-08-12 Single-Chain Molecular Dynamics Trajectories and Analysis Code for Human Nuclear Pore Inner-Ring FG-Repeat Sequences doi:10.57760/sciencedb.45988 en This dataset supports a cross-model analysis of regional intrachain contact preferences in four human nuclear pore inner-ring FG-repeat sequences: Nup54N, Nup58N, Nup58C, and Nup62N. Each sequence was simulated as an isolated chain using two all-atom explicit-solvent force-field/water-model combinations, AMBER99SB/OPC and CHARMM36m/TIP3P, resulting in eight molecular dynamics systems.For each system, the final 500 ns analyzed in the associated study is provided as a matching structure and analysis-ready protein-only trajectory pair in GRO/XTC format, comprising 25,001 frames at 20 ps intervals. The deposit also contains simulation parameter and topology-related files, trajectory preprocessing commands, analysis code (version 4.1.0-public), CALVADOS and Mpipi FINCHES matrices, machine-readable results, validation reports, software-environment records, and a SHA-256 checksum manifest.The analyses include global conformational dimensions, side-chain-heavy-atom binary contacts, sequence-separation-normalized C-alpha distances, sliding-window regional evidence, cross-model residue-pair and chemical-class comparisons, chemical-class observed/expected enrichment, temporal-block support, and parameter-sensitivity analyses. File definitions and reproduction instructions are documented in README.md and DATA_DICTIONARY.md.The deposit contains computational molecular-simulation data only and does not include personal, clinical, geographic, or human-subject data. nuclear pore complex; FG-repeat sequences; nucleoporins; intrinsically disordered proteins; molecular dynamics simulation; intrachain contacts; force-field comparison; reproducible research 鲍徐渊 PUBLIC https://creativecommons.org/licenses/by/4.0/ dataset Science Data Bank