Martinize2 and Vermouth provide a unified framework for molecular topology generation
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Abstract
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design by high-throughput (HT) simulations is another forefront of MD. In these areas, the Martini coarse-grained force field, especially the latest version (i.e. v3), is being actively explored because it offers an enhanced spatial-temporal resolution. However, the automation tools for preparing simulations with the Martini force field, accompanying the previous version, were not designed for HT simulations or studies of complex cellular systems. Therefore, they become a major limiting factor. To address these shortcomings, we present the open-source Vermouth python library. Vermouth is designed to become the unified framework for developing programs, which prepare, run, and analyze Martini simulations of complex systems. To demonstrate the power of the Vermouth library, the Martinize2 program is showcased as a generalization of the martinize script, originally aimed to set up simulations of proteins. In contrast to the previous version, Martinize2 automatically handles protonation states in proteins and post-translation modifications, offers more options to fine-tune structural biases such as the elastic network (EN), and can convert non-protein molecules such as ligands. Finally, Martinize2 is used in two high-complexity benchmarks. The entire I-TASSER protein template database as well as a subset of 200,000 structures from the AlphaFold Protein Structure Database are converted to CG resolution and we illustrate how the checks on input structure quality can safeguard HT applications.
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Hilpert, C., Beranger, L., Souza, P. C. T., Vainikka, P. A., Nieto, V., Marrink, S. J., Monticelli, L., & Launay, G. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c01375 · Cited by 51 · see citing works
Self-citationHoubraken, M., Demeyer, S., Michoel, T., Audenaert, P., Colle, D., & Pickavet, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097896 · Cited by 47 · see citing works
Pedersen, K. B., Borges-Araújo, L., Stange, A. D., Souza, P. C. T., Marrink, . J., & Schiøtt, B. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c00553 · Cited by 41 · see citing works
Self-citationPerspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations
Souza, P. C. T., Limongelli, V., Wu, S., Marrink, S., & Monticelli, L. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.657222 · Cited by 37 · see citing works
Self-citationHoobas: A highly object-oriented builder for molecular dynamics
Girard, M., Ehlen, A., Shakya, A., Bereau, T., & de la Cruz, M. O. (2019) · Computational Materials Science · doi:10.1016/j.commatsci.2019.05.003 · Cited by 37 · see citing works
Demeyer, S., Michoel, T., Fostier, J., Audenaert, P., Pickavet, M., & Demeester, P. M. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061183 · Cited by 32 · see citing works
Sousa, F. M., Lima, L. M. P., Arnarez, C., Pereira, M. M., & Melo, M. N. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c01077 · Cited by 30 · see citing works
SIDUS—the solution for extreme deduplication of an operating system
QuemenerEmmanuel, & CorvellecMarianne (2013) · Linux journal · doi:10.5555/2555789.2555792 · Cited by 30 · see citing works
Integrative structural modelling and visualisation of a cellular organelle
Autin, L., Barbaro, B. A., Jewett, A. I., Ekman, A. A., Verma, S., Olson, A. J., & Goodsell, D. S. (2022) · QRB Discovery · doi:10.1017/qrd.2022.10 · Cited by 26 · see citing works
When computational pipelines go ‘clank’
Marx, V. (2020) · Nature Methods · doi:10.1038/s41592-020-0886-9 · Cited by 19 · see citing works
Martini 3 OliGomers: A Scalable Approach for Multimers and Fibrils in GROMACS
Korshunova, K., Kiuru, J., Liekkinen, J., Enkavi, G., Vattulainen, I., & Bruininks, B. M. H. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c00677 · Cited by 14 · see citing works
SIDUS—the solution for extreme deduplication of an operating system
Quémener, E., & Corvellec, M. (2013) · Linux journal · Cited by 14 · see citing works
MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies
Brasnett, C., & Marrink, . J. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c02277 · Cited by 13 · see citing works
Self-citationEnumerating common molecular substructuresPreprint
Engler, M. S., El-Kebir, M., Mulder, J., Mark, A. E., Geerke, D. P., & Klau, G. W. (2017) · doi:10.7287/peerj.preprints.3250v1 · Cited by 11 · see citing works
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules
Engler, M. S., Caron, B., Veen, L. E., Geerke, D. P., Mark, A. E., & Klau, G. W. (2018) · Centrum Wiskunde & Informatica (CWI), the national research institute for mathematics and computer science in the Netherlands · doi:10.4230/lipics.wabi.2018.16 · Cited by 11 · see citing works
CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions
Grünewald, F., Seute, L., Alessandri, R., König, M., & Kroon, P. C. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c00064 · Cited by 10 · see citing works
Self-citationBioExcel Whitepaper on Scientific Software Development
Abraham, M., Melquiond, A. S. J., Ippoliti, E., Gapsys, V., Hess, B., Trellet, M. E., Rodrigues, J., Laure, E., Apostolov, R., de Groot, B. L., et al. (2018) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.1194633 · Cited by 6 · see citing works
Alibay, I., Barnoud, J., Beckstein, O., Gowers, R. J., Naughton, F. B., & Wang, L. (2022) · Figshare · doi:10.6084/m9.figshare.20520726 · Cited by 3 · see citing works
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Martini 3 Coarse-Grained Force Field for Cholesterol.
Borges-Araújo, L., Borges-Araújo, A. C., Ozturk, T. N., Ramírez-Echemendia, D. P., Fábián, B., Carpenter, T., Thallmair, S., Barnoud, J., Ingólfsson, H., Hummer, G., et al. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00547 · Cited by 71 · see citing works
Self-citationMartini3-IDP: improved Martini 3 force field for disordered proteins
Wang, L., Brasnett, C., Borges-Araújo, L., Souza, P. C. T., & Marrink, . J. (2025) · Nature Communications · doi:10.1038/s41467-025-58199-2 · Cited by 64 · see citing works
Self-citationFacilitating CG Simulations with MAD: The MArtini Database Server
Hilpert, C., Beranger, L., Souza, P. C. T., Vainikka, P. A., Nieto, V., Marrink, S. J., Monticelli, L., & Launay, G. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c01375 · Cited by 51 · see citing works
Self-citationAccurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference
Hoff, S. E., Thomasen, F. E., Lindorff‐Larsen, K., & Bonomi, M. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012180 · Cited by 41 · see citing works
Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2
Bieker, S., Timme, M., Woge, N., Hassan, D., Brown, C. M., Marrink, . J., Melo, M. N., & Holthuis, J. C. M. (2025) · Communications Biology · doi:10.1038/s42003-025-07551-9 · Cited by 30 · see citing works
Mehta, N., Mondal, S., Watson, E. T., Cui, Q., & Chapman, E. R. (2024) · Nature Communications · doi:10.1038/s41467-023-44414-5 · Cited by 28 · see citing works
Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain
Kefauver, J. M., Hakala, M., Zou, X., Alba, J., Espadas, J., Tettamanti, M. G., Gajić, J., Gabus, C., Campomanes, P., Estrozi, L. F., et al. (2024) · Nature · doi:10.1038/s41586-024-07720-6 · Cited by 27 · see citing works
Multiphasic condensates formed with mono-component of tetrapeptides via phase separation
Zhou, L., Zhu, L., Wang, C., Xu, T., Wang, J., Zhang, B., Zhang, X., & Wang, H. (2025) · Nature Communications · doi:10.1038/s41467-025-58060-6 · Cited by 26 · see citing works
CLCC1 promotes hepatic neutral lipid flux and nuclear pore complex assembly
Mathiowetz, A. J., Meymand, E. S., Parlakgül, G., van Hilten, N., Torres, E. F., Artico, L. L., Deol, K. K., Lange, M., Pang, S. P., Doubravsky, C. E., et al. (2026) · Nature · doi:10.1038/s41586-025-10064-4 · Cited by 26 · see citing works
Prediction of Small-Molecule Partitioning into Biomolecular Condensates from Simulation
Emelianova, A., Garcia, P. L., Tan, D., & Joseph, J. A. (2025) · JACS Au · doi:10.1021/jacsau.5c00291 · Cited by 23 · see citing works
Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7
Linhartova, K., Falginella, F. L., Mátl, M., Šebesta, M., Vácha, R., & Štefl, R. (2024) · Nature Communications · doi:10.1038/s41467-024-53305-2 · Cited by 22 · see citing works
Park, P., Matsubara, D. K., Barzotto, D. R., Lima, F. S., Chaimovich, H., Marrink, . J., & Cuccovia, I. M. (2024) · Scientific Reports · doi:10.1038/s41598-024-60601-w · Cited by 21 · see citing works
Soni, J., Gupta, S., & Mandal, T. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c00645 · Cited by 19 · see citing works
Bartocci, A., Grazzi, A., Awad, N., Corringer, P., Souza, P. C. T., & Cecchini, M. (2024) · Nature Communications · doi:10.1038/s41467-024-53098-4 · Cited by 17 · see citing works
Self-citationNonspecific Yet Selective Interactions Contribute to Small Molecule Condensate Binding
Wang, C., Kilgore, H. R., Latham, A. P., & Zhang, B. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01024 · Cited by 16 · see citing works
Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications
Koukos, P. I., Dehghani‐Ghahnaviyeh, S., Velez‐Vega, C., Manchester, J. I., Tieleman, D. P., Duca, J. S., Souza, P. C. T., & Cournia, Z. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00604 · Cited by 16 · see citing works
Self-citationYu, Y., Liu, Q., Zeng, J., Tan, Y., Tang, Y., & Wei, G. (2024) · Chemical Science · doi:10.1039/d4sc03645j · Cited by 14 · see citing works
MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies
Brasnett, C., & Marrink, . J. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c02277 · Cited by 13 · see citing works
Self-citationMartini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?
Hosseini, A., & van der Spoel, D. (2024) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.4c00012 · Cited by 12 · see citing works
Yue, Y., Li, S., Cheng, Y., Wang, L., Hou, T., Zhu, Z., & He, S. (2024) · Nature Communications · doi:10.1038/s41467-024-53583-w · Cited by 11 · see citing works
UBE2J2 sensitizes the ERAD ubiquitination cascade to changes in membrane lipid saturation
Vrentzou, A., Leidner, F., Schmidt, C. C., Grubmüller, H., & Stein, A. (2025) · Nature Communications · doi:10.1038/s41467-025-64777-1 · Cited by 9 · see citing works
Fast Parametrization of Martini3 Models for Fragments and Small Molecules
Szczuka, M., Pereira, G. P., Walter, L. J., Guéroult, M., Poulain, P., Bereau, T., Souza, P. C. T., & Chavent, M. G. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01178 · Cited by 9 · see citing works
Self-citationNemchinova, M., Schuurman‐Wolters, G. K., Whittaker, J. J., Arkhipova, V., Marrink, . J., Poolman, B., & Guskov, A. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c02662 · Cited by 8 · see citing works
Folded domains impose structural heterogeneity and attenuated dynamics in biomolecular condensates
Wang, L., & Marrink, . J. (2026) · Nature Communications · doi:10.1038/s41467-026-71778-1 · Cited by 8 · see citing works
van Tilburg, M., Marrink, . J., König, M., & Grünewald, F. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00961 · Cited by 8 · see citing works
Self-citationMondal, S., Mangiarotti, A., Dimova, R., & Cui, Q. (2025) · Communications Chemistry · doi:10.1038/s42004-025-01810-w · Cited by 7 · see citing works
Cullen, M., Biancaniello, C., Taškova, K., Miletić, V., Mercadante, D., & Simone, A. D. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.5c22987 · Cited by 7 · see citing works
Roessner, R. A., Floquet, N., & Louet, M. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c00202 · Cited by 7 · see citing works
Osorio-Méndez, J. F., Pardo-Rodriguez, D., Rocha‐Roa, C., Toro, L. J., Muñoz-Tabares, L., Recalde-Reyes, D. P., & Cala, M. P. (2025) · Parasites & Vectors · doi:10.1186/s13071-025-06861-5 · Cited by 6 · see citing works
Zhao, M., Lopes, L. J. S., Sahni, H., Yadav, A., Do, H. N., Reddy, T. J., López, C. A., Neale, C., & Gnanakaran, S. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c05018 · Cited by 5 · see citing works
Compartment‐guided assembly of large‐scale molecular models with Bentopy
Westendorp, M. S. S., Stevens, J., Brown, C., Dommer, A., Wassenaar, T., Bruininks, B., & Marrink, S. (2026) · Protein Science · doi:10.1002/pro.70480 · Cited by 7 · see citing works
Self-citationNiemelä, A., & Koivuniemi, A. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012137 · Cited by 5 · see citing works
Hedger, G., & Yen, H. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.168937 · Cited by 5 · see citing works
Optimized Protein–Excipient Interactions in the Martini 3 Force Field
Prass, T. M., Lindorff‐Larsen, K., Garidel, P., Blech, M., & Schäfer, L. V. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c02338 · Cited by 5 · see citing works
Jiang, Y., & Ha‐Duong, T. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c00212 · Cited by 6 · see citing works
Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE
Liu, Y., Brown, C. M., Borges, N., Nobre, R. N., Erramilli, S. K., Dufrisne, M. B., Kloss, B., Giacometti, S. I., Esteves, A. M., Timóteo, C. G., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57843-1 · Cited by 5 · see citing works
Sharma, A., Maurya, S., Tripathi, T., & Padhi, A. K. (2024) · Acta Tropica · doi:10.1016/j.actatropica.2024.107444 · Cited by 5 · see citing works
Delineating the shape of COat Protein complex-II coated membrane bud
Paul, S., Audhya, A., & Cui, Q. (2024) · bioRxiv · doi:10.1093/pnasnexus/pgae305 · Cited by 5 · see citing works
Oqua, A. I., Chao, K., Eid, L. E., Casteller, L., Miguéns, A., Barg, S., Jones, B. J., de la Serna, J. B., Rouse, S. L., & Tomás, A. (2024) · eLife · doi:10.7554/elife.101011.1 · Cited by 4 · see citing works
CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations
Blow, K. E., Parrag, M., & Stansfeld, P. J. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c02066 · Cited by 3 · see citing works
TMEM170 proteins are lipid scramblases associated with bridge-type lipid transporters BLTP1/Csf1
Rocha‐Roa, C., Blair, P. C., Sidhu, G., Álvarez, D., Davey, M., Conibear, E., & Vanni, S. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01716-0 · Cited by 5 · see citing works
Linnik, D., Sultanji, S., Stevens, J. A., Schuurman‐Wolters, G. K., de Boer, R., Punter, C. M., Marrink, . J., Maslov, I., & Poolman, B. (2026) · Nature Communications · doi:10.1038/s41467-026-69951-7 · Cited by 3 · see citing works
Structural basis of signal peptide recognition by the signal peptidase complex
Liaci, A. M., Vismpas, D., Kjølbye, L. R., Skalidis, I., Pereira, G. P., Koh, F., Gröllers‐Mulderij, M., Kotecha, A., Souza, P. C. T., & Förster, F. G. (2026) · Nature Communications · doi:10.1038/s41467-026-73423-3 · Cited by 3 · see citing works
Self-citationBigting, K. V., Nag, S., & An, Y. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c02903 · Cited by 2 · see citing works
Costafrolaz, J., Degeorges, L., Panis, G., Vallet, S.-U., Gomariz, M. V., Meireles, F. T. P., Peraro, M. D., Fröhlich, K. S., & Viollier, P. H. (2026) · The EMBO Journal · doi:10.1038/s44318-025-00668-x · Cited by 3 · see citing works
Sarter, T., Karavalasi, A., & Friess, W. (2026) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.5c01525 · Cited by 2 · see citing works
Li, J., Guo, H., & Song, C. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01859 · Cited by 2 · see citing works
The molecular basis of mitochondrial crista formation by the MIC10 complex
Brown, C. M., Wassenaar, T. A., Freyberg, Z., & Marrink, . J. (2026) · Science Advances · doi:10.1126/sciadv.aee8657 · Cited by 2 · see citing works
Self-citationMicroscopically segregated ligand distribution in co-assembled peptide-amphiphile nanofibers
Pial, T. H., Li, Y., & de la Cruz, M. O. (2024) · Soft Matter · doi:10.1039/d4sm00315b · Cited by 2 · see citing works
Coarse-grained modeling of annexin A2-induced microdomain formation on a vesicle
Lindsay, S., & Li, Y. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2024.06.006 · Cited by 2 · see citing works
Hooten, M., Murthy, N. S., Pal, N., Khare, S. D., Gormley, A. J., & Dutt, M. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0247634 · Cited by 2 · see citing works
A Charge-Driven Strategy for Covalent Modification and Modulation of Biomolecular Condensates
Chen, Z., Liu, L., Cattin, J., Knowles, T. P. J., & Bernardes, G. J. L. (2025) · Journal of the American Chemical Society · doi:10.1021/jacs.5c06625 · Cited by 2 · see citing works
SND3 is the membrane insertase within a fungal multipass transloconPreprint
Yang, T.-J., Mukherjee, S., Langer, J. D., Hummer, G., & McDowell, M. A. (2025) · bioRxiv · doi:10.1101/2025.07.08.663624 · Cited by 2 · see citing works
Efficient Protein–Ligand Binding Free Energy Estimation with Coarse-Grained Funnel Metadynamics
Grazzi, A., Brown, C. M., Sironi, M., Marrink, . J., & Pieraccini, S. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01785 · Cited by 1 · see citing works
Li, F., Radhakrishnan, A., Gautam, S., Diaz, G., Sundaram, R. V. K., Coleman, J., Zheng, H., Grushin, K. S., Chavent, M. G., Rothman, J. E., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2523347123 · Cited by 1 · see citing works
Ancestral neuronal receptors are bacterial accessory toxins
Raoelijaona, F., Szczepaniak, J., Schahl, A., Bray, J. E., Zhou, J. C., Baker, L. A., Omari, K. E., Lowe, E. D., Low, Y. S., Rodriguez, C., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-69246-x · Cited by 1 · see citing works
Comparing multislice projections of MD simulations with cryo-EM exposes structural prediction errors
Mohammed, A., Lincoff, J., Natale, A. M., Ophus, C., Grabe, M., Frost, A., & Moss, F. R. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.02.016 · Cited by 1 · see citing works
Improving Conformational Ensembles of Folded Proteins in GoMartini
Kalutskii, M. A., Wilson, C. J., Grubmüller, H., & Igaev, M. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01816 · Cited by 1 · see citing works
Drajkowska, A., & Molski, A. (2026) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c07780 · Cited by 1 · see citing works
Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field
Brasnett, C., Fidlin, M., Duve, T., Thallmair, S., Marrink, . J., & Grünewald, F. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c01107 · Cited by 1 · see citing works
Self-citationCáceres-Quezada, Á., Borroto‐Escuela, D. O., & Fierro, A. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c00308 · Cited by 1 · see citing works
An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies
Olivos-Ramirez, G. E., Cofas‐Vargas, L. F., Marrink, . J., & Poma, A. B. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.04.024 · Cited by 1 · see citing works
Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation
Ramirez, S. C., Shvarev, D., Duarte, P. V., Ahmed, Y., Milach, J., Lang, E., Kuchenbuch, S., Vanni, S., Reggiori, F., Moeller, A., et al. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00802-3 · Cited by 1 · see citing works
MartiniSurf: Automated Simulations of Surface-Immobilized Biomolecular Systems with Martini
Jiménez-García, J. C., López‐Gallego, F., López, X., & Sancho, D. D. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c00953 · Cited by 1 · see citing works
Dehkhoda, F., Chhabra, Y., Whelan, F., Nowell, C. J., Morris, M. J., Furness, S. G. B., & Brooks, A. J. (2026) · The Journal of Immunology · doi:10.1093/jimmun/vkag118 · Cited by 1 · see citing works
Membrane lipid composition and amino acid sequence determine binding of SARS-CoV-2 fusion peptides
Jiménez-Millán, S., Maestro, A., & Sasselli, I. R. (2026) · Journal of Colloid and Interface Science · doi:10.1016/j.jcis.2026.141021 · Cited by 1 · see citing works
Pires, I. S., Gordon, E., Kindopp, A., Stoneman, A. D., Covarrubias, G., Esparza, G. J., Gomerdinger, V. F., Maiorino, L., Suh, H., Irvine, D. J., et al. (2026) · ACS Nano · doi:10.1021/acsnano.6c02817 · Cited by 1 · see citing works
Encounter-State Over-Anchoring Governs Productive PETase Binding on PET Surfaces
Huo, C., Wang, J., & Chu, X. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6c00544 · Cited by 1 · see citing works
Amphipathic β-Sheet-Forming Octapeptide Self-Assembly Using the Martini Potential Family
Maity, D., & Qiao, B. (2026) · ACS Omega · doi:10.1021/acsomega.6c02457 · Cited by 1 · see citing works
Kwon, H., & Li, Y. (2026) · Food Hydrocolloids · doi:10.1016/j.foodhyd.2026.113310 · Cited by 1 · see citing works
Presynaptic accumulation of APP-CTFβ may contribute to synaptic dysfunction in Alzheimer’s disease
Kapadia, A., Schuhmann, F., Daşkın, E., Walter, J., Lindahl, I., Rahmani, N., Morrema, T. H. J., Rozemüller, A. J. M., Boon, B. D. C., Pezeshkian, W., et al. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00899-6 · Cited by 1 · see citing works
Duncan, A. L., Gao, Y., Haanappel, E., Im, W., & Chavent, M. G. (2023) · ChemRxiv · doi:10.26434/chemrxiv-2023-mfc5k · Cited by 1 · see citing works
Mondal, S., Mangiarotti, A., Dimova, R., & Cui, Q. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.16.654554 · Cited by 1 · see citing works
Ceramides disrupt hexokinase HKI-VDAC complex assembly and modulate VDAC tiltingPreprint
Timme, M., Holthuis, J. C. M., & Melo, M. N. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.25.720789 · Cited by 1 · see citing works
Guillén-Samander, A., Ahmed, Y., Ribeiro-Holbein, A., Cubillán-Marín, J., Höhn, K., Rocha‐Roa, C., Dröge, J., Panitzsch, L. S., Burda, P., Gilberger, T., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.11.750981 · Cited by 1 · see citing works
Optimising excipient properties to prevent aggregation in biopharmaceutical formulationsPreprint
King, T., Humphrey, J., Laughton, C. A., Thomas, N. R., & Hirst, J. D. (2023) · ChemRxiv · doi:10.26434/chemrxiv-2023-rgvlz
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- Authors
- Kroon, P. C., Grünewald, F., Barnoud, J., van Tilburg, M., Brasnett, C., Souza, P. C., Wassenaar, T. A., & Marrink, S. J.
- Affiliations
- University of Groningen (NL)
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen
- École Normale Supérieure de Lyon (FR)
- Corresponding author
- Grünewald, Fabian
- Marrink, Siewert J
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2025-11-20
- Volume
- 12
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC12634043
- OpenAlex
- W7106126080
- Cited by
- 124
- References
- 104
- Citations by year
- 2026: 73 · 2025: 22 · 2024: 22 · 2023: 7
- Type
- posted content
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, cc-by)
- arXiv (Cornell University) (submittedVersion)
- HAL (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- arXiv (Cornell University) (cc-by)
- Funders
- European Research Council (COMP-MICR-CROW-MEM)
- Novo Nordisk (BOUNDLESS)
- Klaus Tschira Foundation (Independent Postdoc)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- Martini coarse-grained force field, vermouth, high-throughput molecular dynamics, protonation states, post-translational modification, elastic networks, AlphaFold structures
- MeSH terms
- Proteins, Software, Molecular Dynamics Simulation
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