Martini 3

Autor: Vincent Nieto, Valentina Corradi, Siewert J. Marrink, Matti Javanainen, Peter C. Kroon, Ilpo Vattulainen, Hector Martinez-Seara, D. Peter Tieleman, Alex H. de Vries, Jan Domański, Hanif M. Khan, Robert B. Best, Ilias Patmanidis, Sebastian Thallmair, Ignacio Faustino, Xavier Periole, Jonathan Barnoud, Tsjerk A. Wassenaar, Josef Melcr, Nathalie Reuter, Haleh Abdizadeh, Bart M H Bruininks, Paulo C. T. Souza, Fabian Grünewald, Riccardo Alessandri, Luca Monticelli

Publikováno v: Nature Methods, 18, 382-388. Nature Publishing Group
Nature Methods
Souza, P C T, Alessandri, R, Barnoud, J, Thallmair, S, Faustino, I, Grünewald, F, Patmanidis, I, Abdizadeh, H, Bruininks, B M H, Wassenaar, T A, Kroon, P C, Melcr, J, Nieto, V, Corradi, V, Khan, H M, Domański, J, Javanainen, M, Martinez-Seara, H, Reuter, N, Best, R B, Vattulainen, I, Monticelli, L, Periole, X, Tieleman, D P, de Vries, A H & Marrink, S J 2021, ' Martini 3 : a general purpose force field for coarse-grained molecular dynamics ', Nature Methods, vol. 18, no. 4, pp. 382-388 . https://doi.org/10.1038/s41592-021-01098-3

The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific inter

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f1fe1d2646ea2c4aa330b9fd3b0ab46d
https://hdl.handle.net/11370/27f1d65b-ff4d-4290-9fc8-b019e36c5c2e

Atomistic mechanism of transmembrane helix association

Autor: Phillip J. Stansfeld, Robert B. Best, Mark S.P. Sansom, Jan Domański

Publikováno v: PLoS Computational Biology
PLoS Computational Biology, Vol 16, Iss 6, p e1007919 (2020)

Transmembrane helix association is a fundamental step in the folding of helical membrane proteins. The prototypical example of this association is formation of the glycophorin dimer. While its structure and stability have been well-characterized expe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::37914d834eb439d8e4f474e6c1763eaa
https://pubmed.ncbi.nlm.nih.gov/32497094

Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association

Autor: Jan, Domański, Mark S P, Sansom, Phillip J, Stansfeld, Robert B, Best

Publikováno v: Journal of Chemical Theory and Computation

Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold globular proteins and have provided insights into folding mechanisms. Gaining similar understanding from simulations of membrane protein folding and associa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::75525eb6a639856cc70a77846d191d0b
https://pubmed.ncbi.nlm.nih.gov/29424543

Structural propensity database of proteins

Autor: Jan Domański, Kamil Tamiola, Matthew M. Heberling

An overwhelming amount of experimental evidence suggests that elucidations of protein function, interactions, and pathology are incomplete without inclusion of intrinsic protein disorder and structural dynamics. Thus, to expand our understanding of i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::349c0053b278c93cd112170cae35b902

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations

Autor: Jan Domański, Sean L. Seyler, David L. Dotson, Sébastien Buchoux, Max Linke, Richard Gowers, Manuel N. Melo, Ian M. Kenney, Jonathan Barnoud, Oliver Beckstein, Tyler Reddy

Publikováno v: Proceedings of the Python in Science Conference.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::09e146fa019a5336366d1d491c89929c
https://doi.org/10.25080/majora-629e541a-00e