ArticlebioRxiv : the preprint server for biology2025
How Well Do Molecular Dynamics Force Fields Model Peptides? A Systematic Benchmark Across Diverse Folding Behaviors.
Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Linear peptides play essential roles in biology and drug discovery, frequently mediating protein-protein interactions through short, flexible motifs. However, their structural plasticity-ranging from disordered to context-dependent folding-makes them challenging targets for molecular simulations. In this work, we benchmark the performance of twelve popular and emerging fixed-charge force fields across a curated set of twelve peptides spanning structured miniproteins, context-sensitive epitopes, and disordered sequences. Each peptide was simulated from both folded (200 ns) and extended (10
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