E. Diamanti, P.C.T. Souza, I. Setyawati, S. Bousis, L.M. Gómez, L.J.Y.M. Swier, ..., S.J Marrink, D.J. Slotboom, A.K.H. Hirsch.Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Commun. Biology 6 (1), 1182, 2023. doi:10.1038/s42003-023-05555-x
H.I. Ingólfsson, A. Rizuan, X. Liu, P. Mohanty, P.C.T. Souza, S.J. Marrink, M.T. Bowers, J. Mittal, J. Berry.Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation. Biophys. J. 122, 4370-4381, 2023. doi:10.1016/j.bpj.2023.10.016
M. Manrho, S.R. Krishnaswamy, B. Kriete, I. Patmanidis, A.H. de Vries, S.J. Marrink, T.L.C. Jansen, J. Knoester, M.S. Pshenichnikov. Watching Molecular Nanotubes Self-Assemble in Real Time. J. Amer. Chem. Soc. 145 (41), 22494–22503, 2023. doi:10.1021/jacs.3c07103
L. Borges-Araújo, I. Patmanidis, A.P. Singh, L.H.S. Santos, A.K. Sieradzan, S. Vanni, C. Czaplewski, S. Pantano, W. Shinoda, L. Monticelli, A. Liwo, S.J. Marrink, P.C.T. Souza.Pragmatic Coarse-Graining of Proteins: Models and Applications. J. Chem. Theory Comput. 19 (20), 7112-7135, 2023. doi:10.1021/acs.jctc.3c00733
L. Borges-Araújo, A. Borges-Araújo, T. Ozturk, D.P. Ramirez-Echemendia, B. Fábián, T.S. Carpenter, S. Thallmair, J. Barnoud, H.I. Ingólfsson, G. Hummer, D.P. Tieleman, S.J. Marrink, P.C.T. Souza, M.N. Melo.Martini 3 Coarse-Grained Force Field for Cholesterol. J. Chem. Theory Comput. 19 (20), 7387-7404, 2023. doi:10.1021/acs.jctc.3c00547
A. Tharmasothirajan, J. Melcr, J. Linney, T. Gensch, K. Krumbach, K.M. Ernst, C. Brasnett, P. Poggi, A.R. Pitt, A.D. Goddard, A. Chatgilialoglu, S.J. Marrink, J. Marienhagen.Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis. Nature Commun. 14 (1), 5619, 2023. doi:10.1038/s41467-023-40947-x
P.C. Kroon, F. Grünewald, J. Barnoud, M. van Tilburg, P.C.T. Souza, T.A. Wassenaar, S.J. Marrink.Martinize2 and Vermouth: Unified Framework for Topology Generation. eLife 12, RP90627, 2023. doi:10.7554/eLife.90627.1
C. Thangaratnarajah, M. Nijland, L. Borges-Araújo, A. Jeucken, J. Rheinberger, S.J. Marrink, P.C.T. Souza, C. Paulino, D.J. Slotboom.Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nature Commun. 14, 4484, 2023. doi:10.1038/s41467-023-40266-1
A. Blanco-González, S.J. Marrink, Á. Piñeiro, R. García-Fandiño.Molecular insights into the effects of focused ultrasound mechanotherapy on lipid bilayers: unlocking the keys to design effective treatments. J. Colloid Interf. Sci. 650 (B), 1201-1210, 2023. doi:10.1016/j.jcis.2023.07.077
B.R. Gilbert, Z.R. Thornburg, T.A. Brier, J.A. Stevens, F. Grunewald, J.E. Stone, S.J. Marrink, Z.A. Luthey-Schulten.Dynamics of Chromosome Organization in a Minimal Bacterial Cell. Front. Cell Dev. Biol., 2023, online. doi:10.3389/fcell.2023.1214962
A. Melcrova, S. Maity, J. Melcr, N.A.W. de Kok, M. Gabler, J. van der Eyden, W. Stensen, J.S M. Svendsen, A.J.M. Driessen, S.J. Marrink, W.H. Roos.Lateral membrane organization as target of an antimicrobial peptidomimetic compound. Nature Commun. 4, 4038, 2023. doi:10.1038/s41467-023-39726-5
S. Sami, S.J. Marrink. Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations. J. Chem. Theory Comput., 19 (13), 4040–4046, 2023. doi:10.1021/acs.jctc.2c01186
M. Ren, L. Zhao, Z. Ma, H. An, S.J. Marrink, F. Sun.Molecular basis of PIP2-dependent conformational switching of phosphorylated CD44 in binding FERM. Biophys. J., 122 (13), 2675-2685, 2023. doi:10.1016/j.bpj.2023.05.021
C. Empereur-Mot, K.B. Pedersen, C. Caruso, M. Perrone, M. Crippa, P.C.T. Souza, S.J. Marrink, G.M. Pavan.On the Automatic Optimization of Lipid Models in the Martini Force Field using SwarmCG. J. Chem. Inf. Model. 63 (12), 3827–3838, 2023. doi:10.1021/acs.jcim.3c00530
W. Pezeshkian, F. Grünewald, O. Narykov, S. Lu, T.A. Wassenaar, S.J. Marrink, D. Korkin.Molecular architecture of SARS-CoV-2 envelope by integrative modeling. Structure 31 (4), 492-503, 2023. doi:10.1016/j.str.2023.02.006
S. Sami, F. Grünewald, P.C.T. Souza, S.J. Marrink,A Guide to Titratable Martini Simulations, in A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules [AIP Publishing (online), Melville, New York, 2023], available at: doi:10.1063/9780735425279_004.
R. Alessandri, S. Thallmair, C.G. Herrero, R. Mera- Adasme, S.J. Marrink, P.C.T. Souza, A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations, in A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules [AIP Publishing (online), Melville, New York, 2023]. doi:10.1063/9780735425279_001
C. Hilpert, L. Beranger, P.C.T. Souza, P.A. Vainikka, V. Nieto, S.J. Marrink, L. Monticelli, G. Launay.Facilitating CG Simulations with MAD: The MArtini Database Server. J. Chem. Inf. Model., 63 (3), 702–710, 2023. doi:10.1021/acs.jcim.2c01375
M.G. Chiariello, F. Grünewald, R. Zarmiento-Garcia, S.J. Marrink.pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. J. Phys. Chem. Lett. 14, 905-911, 2023. doi:10.1021/acs.jpclett.2c03760
J.A. Stevens, F. Grünewald, P.A.M. van Tilburg, M. König, B.R. Gilbert, T.A. Brier, Z.R. Thornburg, Z. Luthey-Schulten, S.J. Marrink.Molecular dynamics simulation of an entire cell. Frontiers in Chemistry 11, 2023. doi:10.3389/fchem.2023.1106495
P. Vainikka, S.J. Marrink.Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches. J. Chem. Theory Comput., 2023, online. doi:org/10.1021/acs.jctc.2c00796
B. Waclawiková, P.C.T. Souza, M. Schwalbe, C.G. Neochoritis, W. Hoornenborg, S.A. Nelemans, S.J. Marrink, S. El Aidy. Potential binding modes of the gut bacterial metabolite, 5-hydroxyindole, to the intestinal L-type calcium channels and its impact on the microbiota in rats. Gut Microbes 15 (1), 2154544, 2023. doi:10.1080/19490976.2022.2154544
S.J. Marrink, L. Monticelli, M.N. Melo, R. Alessandri, D.P. Tieleman, P.C.T. Souza.Two decades of Martini: Better beads, broader scope. Wires Computational Molecular Science, 13(1), e1620, 2023. https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1620
N. De Franceschi, W. Pezeshkian, A. Fragasso, B.M.H. Bruininks, S. Tsai, S.J. Marrink, C. Dekker.Synthetic Membrane Shaper for Controlled Liposome Deformation. ACS Nano, online, 2023. doi:10.1021/acsnano.2c06125
