Coarse-grained simulations of long intrinsically disordered proteins: a benchmark of Martini 3 force-fields

2026/07/17 by Christina Goss, Camilo Aponte‐Santamaría, Frauke Gräter · 1 voice
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · Environmental Science · #Protein Structure and Dynamics #Force Microscopy Techniques and Applications #Bacteriophages and microbial interactions

paper · pdf · doi:10.64898/2026.07.17.739185

Abstract

Abstract Martini 3 is a force field ideally suited to simulating long intrinsically disordered proteins (IDPs) in cell-like surroundings. So far, most Martini 3 variations intended for IDPs have only been benchmarked on shorter IDPs of up to 140 amino acids. In this paper, we present a comprehensive benchmark including IDPs up to 809 amino acids in length and compare the behavior of four well-known Martini 3 variations for IDPs. Modifications to only the bonded parameters result in excessively compact conformations, thereby failing to reproduce the experimental radius of gyration observed for large IDPs. In contrast, general rescaling of interaction parameters, including tuning electrostatic interactions in the case of highly-charged long IDPs, yields acceptable levels of compaction at all tested length scales.

Discussions

• It's nice when you benchmark your own method and find it good. But its even nicer when others benchmark your method and find it good. Figure from: Coarse-grained simulations of long intrinsically dis [bsky, 17 points, 1 comments]

Related

• Fine structures of Intrinsically Disordered Proteins
• Room for Improvement in the Initial Martini 3 Parameterization of Peptide Interactions
• The Protein Force Field Plays a Crucial Role in Obtaining Accurate Macromolecular Ensembles of IDPs
• The Martini Model in Materials Science
• Current Topics, Methods, and Challenges in the Modelling of Intrinsically Disordered Protein Dynamics