TY  - INPR
A1  - Souza, Paulo Cesar Telles de
A1  - Borges Araujo, Luis P.
A1  - Brasnett, Chris
A1  - Silva, Rodrigo Azevedo Moreira da
A1  - Grünewald, Fabian
A1  - Park, Peter
A1  - Wang, Liguo
A1  - Razmazma, Hafez
A1  - Araújo, Ana Carolina Borges
A1  - Cofas-Vargas, Luis Fernando
A1  - Monticelli, Luca
A1  - Mera-Adasme, Raul
A1  - Melo, Manuel Nuno
A1  - Wu, Sangwook
A1  - Marrink, Siewert J.
A1  - Poma, Adolfo B.
A1  - Thallmair, Sebastian
T1  - GoMartini 3: From large conformational changes in proteins to environmental bias corrections
T2  - bioRxiv
N2  - 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 new 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.
Y1  - 2024
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/83812
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-838121
UR  - https://www.biorxiv.org/content/10.1101/2024.04.15.589479v1
IS  - 2024.04.15.589479 Version 1
PB  - bioRxiv
ER  -