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Published October 16, 2026 | Version v1
Dataset Open

Imperial College 2026: reGELerate: all-atom MD trajectories of a capped HET-s fibril with attached and free Cys–maleimide–PEG12–biotin

Authors/Creators

  • 1. Imperial College London

Description

All-atom molecular dynamics trajectories made by Team Imperial College, iGEM 2026 (Imperial College London) as reference data for a coarse-grained model of a functionalised amyloid fibril, fitted with multi-state iterative Boltzmann inversion (MS-IBI).

The system is an 11-chain HET-s(218–289) fibril with an engineered cap docked on one end, carrying the non-canonical residue CYL (cysteine–maleimide–PEG12–biotin). Four simulations: the capped fibril alone in water (150 ns); one capped CYL in water (1 ns); the fibril with CYL attached at two sites (200 ns); the fibril among 40 free capped CYL molecules (200 ns). Amber ff19SB, GAFF2, OPC water, 298 K, GROMACS 2026.3. Solute-only trajectories are included (the full-system trajectories with water and ions are too large and are available on request), with every run's GROMACS input, topology, energy and log files.

README.md describes every file, how the runs were set up, how to read them, and their known limitations.

Code: NCAAP-MDF on iGEM GitLab. Wiki: https://2026.igem.wiki/imperial-college/. Contact: Harvey Fung, harveyfunghf@gmail.com.

Files

free_files.zip

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Additional details

Related works

Is supplemented by
Software: https://gitlab.igem.org/2026/software/imperial-college/full-atom-trajectory-for-msibi (URL)

References

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