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bioRxiv · 10.64898/2026.03.16.712088

drFrankenstein: An Automated Pipeline for the Parameterisation of Non-Canonical Amino Acids

Shrimpton-Phoenix, E.·Notari, E.·Wood, C. W.
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Abstract

The incorporation of non-canonical amino acids (ncAAs) is a powerful strategy for introducing novel chemical functions into proteins. Molecular dynamics (MD) simulations are essential for understanding the structural and dynamic effects of these modifications, yet the creation of accurate force field parameters for ncAAs remains a significant bottleneck. Current parameterisation methods are often inaccurate or computationally expensive. To address this, we present drFrankenstein, an automated pipeline for generating AMBER force field parameters for ncAAs. drFrankenstein is a robust and accessible tool that streamlines the parameterisation workflow, enabling the routine use of MD simulations to study the behaviour of ncAA-containing proteins.

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Shrimpton-Phoenix, E., Notari, E., Wood, C. W.. 2026-03-18. drFrankenstein: An Automated Pipeline for the Parameterisation of Non-Canonical Amino Acids. https://doi.org/10.64898/2026.03.16.712088

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