GōMartini 3: From large conformational changes in proteins to environmental bias corrections

Paulo C. T. Souza (), Luís Borges-Araújo, Christopher Brasnett, Rodrigo A. Moreira, Fabian Grünewald, Peter Park, Liguo Wang, Hafez Razmazma, Ana C. Borges-Araújo, Luis Fernando Cofas-Vargas, Luca Monticelli, Raúl Mera-Adasme, Manuel N. Melo, Sangwook Wu, Siewert J. Marrink (), Adolfo B. Poma () and Sebastian Thallmair ()
Additional contact information
Paulo C. T. Souza: 46 Allée d’Italie
Luís Borges-Araújo: 46 Allée d’Italie
Christopher Brasnett: Nijenborgh 7
Rodrigo A. Moreira: P812
Fabian Grünewald: Schloss-Wolfsbrunnenweg 35
Peter Park: Nijenborgh 7
Liguo Wang: Nijenborgh 7
Hafez Razmazma: 7 Passage du Vercors
Ana C. Borges-Araújo: Av. da República
Luis Fernando Cofas-Vargas: 02-106
Luca Monticelli: 7 Passage du Vercors
Raúl Mera-Adasme: Universidad de Tarapacá
Manuel N. Melo: Av. da República
Sangwook Wu: PharmCADD
Siewert J. Marrink: Nijenborgh 7
Adolfo B. Poma: 02-106
Sebastian Thallmair: Ruth-Moufang-Straße 1

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access to spatio-temporal scales beyond all-atom based approaches. The GōMartini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency and accurate representation of protein dynamics with the capabilities of studying proteins in different biological environments. This paper introduces an enhanced GōMartini model, which combines a virtual-site implementation of Gō models with Martini 3. The implementation has been extensively tested by the community since the release of the reparametrized version of Martini. This work demonstrates the capabilities of the model in diverse case studies, ranging from protein-membrane binding to protein-ligand interactions and AFM force profile calculations. The model is also versatile, as it can address recent inaccuracies reported in the Martini protein model. Lastly, the paper discusses the advantages, limitations, and future perspectives of the Martini 3 protein model and its combination with Gō models.

Date: 2025
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DOI: 10.1038/s41467-025-58719-0

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