20.500.12556/DKUM-92203 Enhancing Martini3 for protein self-interaction simulations Coarse-grained molecular dynamics simulations are highly valuable for studying protein-protein interactions. Unfortunately, commonly used force fields often overestimate these interactions. Here, we investigate the performance of the Martini 3 force field in predicting the self-interaction behavior of lysozyme and subtilisin using Metadynamics. The original Martini 3, despite improvements over its predecessor, overestimates interaction strength. Through reparameterization of bead interactions, we achieve good agreement with experimental data of the second virial coefficient and the diffusion coefficient. The new, refined force field enables more accurate CG-MD simulations, with potential applications in understanding and prediction of protein stability, aggregation tendencies, and solubility, with the possibility to aid in the development of protein-based drugs. coarse-grained molecular dynamics Martini 3 force field protein-protein interactions B22 reparameterization NMR diffusion coefficient molekularna dinamika interakcija proteinov reparameterizacija true false true Elsevier Angleški jezik Slovenski jezik https://www.sciencedirect.com/journal/european-journal-of-pharmaceutical-sciences © 2025 The Authors Članek v reviji 2025-03-20 12:35:12 2025-03-20 12:35:13 2026-01-09 09:06:07 0000-00-00 00:00:00 2025 0 0 28 str. [article no.] 107068 Available online 10 March 2025 0000-00-00 Zaloznikova Objavljeno NiDoloceno 2024-11-14 2025-03-09 2025-03-10 543.2/.9 228983811 10.1016/j.ejps.2025.107068 1879-0720 1-s2.0-S0928098725000673-main.pdf 1-s2.0-S0928098725000673-main.pdf 1 BFF4B77B6ADD7A75886A9BED9A7DFC95 9d96a3290bffef34fbe4ee10119e90884344d0c5f8a49c0188ee49fca08bd703 c184102d-057f-11f0-9be3-00155d000105 https://dk.um.si/Dokument.php?lang=slv&id=189518 https://www.sciencedirect.com/science/article/pii/S0928098725000673?via%3Dihub 0 0d12e236-ed32-11f0-8729-00155d580e02 https://dk.um.si/Dokument.php?lang=slv&id=201856 Fakulteta za kemijo in kemijsko tehnologijo 0 0 0