Publications

Frallicciardi, J., Melcr, J., Siginou, P., Marrink, S. J., & Poolman, B. (2022). Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes. Nature Communications, 13(1), [1605]. https://doi.org/10.1038/s41467-022-29272-x

Patmanidis, I., Souza, P. C. T., Sami, S., Havenith, R. W. A., de Vries, A. H., & Marrink, S. J. (2022). Modelling structural properties of cyanine dye nanotubes at coarse-grained level. Nanoscale advances. https://doi.org/10.1039/d2na00158f

Losa, J., Leupold, S., Alonso-Martinez, D., Vainikka, P., Thallmair, S., Tych, K. M., Marrink, S. J., & Heinemann, M. (2022). Perspective: A stirring role for metabolism in cells. Molecular Systems Biology, 18(4), [e10822]. https://doi.org/10.15252/msb.202110822

Grünewald, F., Alessandri, R., Kroon, P. C., Monticelli, L., Souza, P. C. T., & Marrink, S. J. (2022). Polyply: A python suite for facilitating simulations of macromolecules and nanomaterials. Nature Communications, 13(1), [68]. https://doi.org/10.1038/s41467-021-27627-4

Versloot, R. C. A., Lucas, F. L. R., Yakovlieva, L., Tadema, M. J., Zhang, Y., Wood, T. M., Martin, N. I., Marrink, S. J., Walvoort, M. T. C., & Maglia, G. (2022). Quantification of Protein Glycosylation Using Nanopores. Nano Letters, 22(13), 5357-5364. [2c10338]. https://doi.org/10.1021/acs.nanolett.2c01338

Marrink, S. J., Monticelli, L., Melo, M. N., Alessandri, R., Tieleman, D. P., & Souza, P. C. T. (2022). Two decades of Martini: Better beads, broader scope. Wiley Interdisciplinary Reviews: Computational Molecular Science, [e1620]. https://doi.org/10.1002/wcms.1620

Krishnaswamy, S. R., Gabrovski, I. A., Patmanidis, I., Stuart, M. C. A., de Vries, A. H., & Pshenichnikov, M. S. (2022). Cryogenic TEM imaging of artificial light harvesting complexes outside equilibrium. Scientific Reports, 12(1), [5552]. https://doi.org/10.1038/s41598-022-09496-z

Machado, N., Bruininks, B. M. H., Singh, P., Dos Santos, L., Dal Pizzol, C., Dieamant, G. D. C., Kruger, O., Martin, A. A., Marrink, S. J., Souza, P. C. T., & Favero, P. P. (2022). Complex nanoemulsion for vitamin delivery: Droplet organization and interaction with skin membranes. Nanoscale, 14(2), 506-514. https://doi.org/10.1039/d1nr04610a

Alessandri, R., Barnoud, J., Gertsen, A. S., Patmanidis, I., de Vries, A. H., Souza, P. C. T., & Marrink, S. J. (2022). Martini 3 Coarse-Grained Force Field: Small Molecules. Advanced theory and simulations, 5(1), [2100391]. https://doi.org/10.1002/adts.202100391

Azadi-Chegeni, F., Thallmair, S., Ward, M. E., Perin, G., Marrink, S. J., Baldus, M., Morosinotto, T., & Pandit, A. (2022). Protein dynamics and lipid affinity of monomeric, zeaxanthin-binding LHCII in thylakoid membranes. Biophysical Journal, 121(3), 396-409. [bpj.2021.12.039]. https://doi.org/10.1016/j.bpj.2021.12.039

Stehantsev, P., Stetsenko, A., Nemchinova, M., Aduri, N. G., Marrink, S., Gati, C., & Guskov, A. (2021). A structural view onto disease-linked mutations in the human neutral amino acid exchanger ASCT1. Computational and Structural Biotechnology Journal, 19, 5246-5254. https://doi.org/10.1016/j.csbj.2021.09.015

Nemchinova, M., Melcr, J., Wassenaar, T., Marrink, S., & Guskov, A. (2021). Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. Journal of chemical information and modeling, 61(5), 2407-2417. https://doi.org/10.1021/acs.jcim.1c00261

Kobauri, P., Szymanski, W., Cao, F., Thallmair, S., Marrink, S. J., Witte, M. D., Dekker, F. J., & Feringa, B. L. (2021). Biaryl sulfonamides as cisoid azosteres for photopharmacology. Chemical Communications, 57(34), 4126-4129. https://doi.org/10.1039/d1cc00950h

Zhang, S., Huang, G., Versloot, R. C. A., Bruininks, B. M. H., de Souza, P. C. T., Marrink, S-J., & Maglia, G. (2021). Bottom-up fabrication of a proteasome-nanopore that unravels and processes single proteins. Nature Chemistry, 13(12), 1192–1199. https://doi.org/10.1038/s41557-021-00824-w

Liu, Y., de Vries, A. H., Pezeshkian, W., & Marrink, S. J. (2021). Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 17(9), 5876-5884. [00151]. https://doi.org/10.1021/acs.jctc.1c00151

Tsanai, M., Frederix, PW. J. M., Schroer, C. F. E., Souza, P. C. T., & Marrink, S. J. (2021). Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model. Chemical Science, 12(24), 8521-8530. https://doi.org/10.1039/d1sc00374g

Patmanidis, I., Alessandri, R., de Vries, A. H., & Marrink, S. J. (2021). Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields. Molecules, 26(19), [6069]. https://doi.org/10.3390/molecules26196069

Ramírez-Palacios, C., Wijma, H. J., Thallmair, S., Marrink, S. J., & Janssen, D. B. (2021). Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations. Journal of chemical information and modeling, 61(11), 5569–5580. https://doi.org/10.1021/acs.jcim.1c00617

Meng, Q., Ramírez-Palacios, C., Capra, N., Hooghwinkel, M. E., Thallmair, S., Rozeboom, H. J., Thunnissen, A. M. W. H., Wijma, H. J., Marrink, S. J., & Janssen, D. B. (2021). Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines. ACS Catalysis, 11(17), 10733-10747. https://doi.org/10.1021/acscatal.1c02053

Dong, J., Sami, S., Balazs, D. M., Alessandri, R., Jahani, F., Qiu, L., Marrink, S. J., Havenith, R. W. A., Hummelen, J. C., Loi, M. A., & Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C, 9(45), 16217-16225. https://doi.org/10.1039/d1tc02753k

Kjølbye, L. R., De Maria, L., Wassenaar, T. A., Abdizadeh, H., Marrink, S. J., Ferkinghoff-Borg, J., & Schiøtt, B. (2021). General Protocol for Constructing Molecular Models of Nanodiscs. Journal of chemical information and modeling, 61(6), 2869-2883. [acs.jcim.1c00157]. https://doi.org/10.1021/acs.jcim.1c00157

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., ... Marrink, S. J. (2021). Martini 3: A general purpose force field for coarse-grained molecular dynamics. Nature Methods, 18, 382-388. https://doi.org/10.1038/s41592-021-01098-3

Vainikka, P., Thallmair, S., Souza, P. C. T., & Marrink, S. J. (2021). Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties. ACS Sustainable Chemistry and Engineering, 9(51), 17338-17350. https://doi.org/10.1021/acssuschemeng.1c06521

Thallmair, S., Javanainen, M., Fábián, B., Martinez-Seara, H., & Marrink, S. J. (2021). Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations. Journal of Physical Chemistry B, 125(33), 9537-9546. https://doi.org/10.1021/acs.jpcb.1c03665

Souza, P. C. T., Limongelli, V., Wu, S., Marrink, S. J., & Monticelli, L. (2021). Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Frontiers in Molecular Biosciences, 8, [657222]. https://doi.org/10.3389/fmolb.2021.657222

Yakovlieva, L., Ramírez-Palacios, C., Marrink, S. J., & Walvoort, M. T. C. (2021). Semiprocessive Hyperglycosylation of Adhesin by Bacterial Protein N-Glycosyltransferases. ACS chemical biology, 16(1), 165-175. https://doi.org/10.1021/acschembio.0c00848

Bruininks, B. M. H., Thie, A. S., Souza, P. C. T., Wassenaar, T. A., Faraji, S., & Marrink, S. J. (2021). Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies. Journal of Chemical Theory and Computation, 17(12), 7873–7885. https://doi.org/10.1021/acs.jctc.1c00446

Pezeshkian, W., & Marrink, S. J. (2021). Simulating realistic membrane shapes. Current Opinion in Cell Biology, 71, 103-111. [j.ceb.2021.02.009]. https://doi.org/10.1016/j.ceb.2021.02.009

Liaci, A. M., Steigenberger, B., Telles de Souza, P. C., Tamara, S., Gröllers-Mulderij, M., Ogrissek, P., Marrink, S. J., Scheltema, R. A., & Förster, F. (2021). Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Molecular Cell, 81(19), 3934-3948.e11. https://doi.org/10.1016/j.molcel.2021.07.031

Alessandri, R., Grünewald, F., & Marrink, S. J. (2021). The Martini Model in Materials Science. Advanced materials, 33(24), [e2008635]. https://doi.org/10.1002/adma.202008635

Marjanovic, A., Ramírez-Palacios, C. J., Masman, M. F., Drenth, J., Otzen, M., Marrink, S-J., & Janssen, D. B. (2021). Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase. Protein Engineering, Design & Selection, 34, [gzab016]. https://doi.org/10.1093/protein/gzab016

Piskorz, T. K., de Vries, A. H., & van Esch, J. H. (2022). How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers. Journal of Chemical Theory and Computation, 18(1), 431-440. [acs.jctc.1c00257]. https://doi.org/10.1021/acs.jctc.1c00257

Yildirim, A., Tekpinar, M., & Wassenaar, T. A. (2021). Competing Roles of Ca²⁺and Nonmuscle Myosin IIA on the Dynamics of the Metastasis-Associated Protein S100A4. Journal of Physical Chemistry B, 125(36), 10059-10071. [02096]. https://doi.org/10.1021/acs.jpcb.1c02096

Molenaar, M. R., Yadav, K. K., Toulmay, A., Wassenaar, T. A., Mari, M. C., Caillon, L., Chorlay, A., Lukmantara, I. E., Haaker, M. W., Wubbolts, R. W., Houweling, M., Vaandrager, A. B., Prieur, X., Reggiori, F., Choudhary, V., Yang, H., Schneiter, R., Thiam, A. R., Prinz, W. A., & Helms, J. B. (2021). Retinyl esters form lipid droplets independently of triacylglycerol and seipin. The Journal of Cell Biology, 220(10), [202011071]. https://doi.org/10.1083/jcb.202011071

Bruininks, B. M., Souza, P. C., Ingolfsson, H., & Marrink, S. J. (2020). A molecular view on the escape of lipoplexed DNA from the endosome. eLife, 9, [e52012]. https://doi.org/10.7554/eLife.52012

Dong, L., Meng, Q., Ramirez-Palacios, C., Wijma, H. J., Marrink, S. J., & Janssen, D. B. (2020). Asymmetric synthesis of optically pure aliphatic amines with an engineered robust ω-transaminase. Catalysts, 10(11), 1-14. [1310]. https://doi.org/10.3390/catal10111310

Pezeshkian, W., König, M., Wassenaar, T. A., & Marrink, S. J. (2020). Backmapping triangulated surfaces to coarse-grained membrane models. Nature Communications, 11(1), [2296]. https://doi.org/10.1038/s41467-020-16094-y

Khan, H. M., Telles de Souza, P. C., Thallmair, S., Barnoud, J., De Vries, A. H., Marrink, S. J., & Reuter, N. (2020). Capturing Choline–Aromatics Cation−π Interactions in the MARTINI Force Field. Journal of Chemical Theory and Computation, 16(4), 2550-2560. https://doi.org/10.1021/acs.jctc.9b01194

Maity, S., Ottelé, J., Santiago, G. M., Frederix, P. W. J. M., Kroon, P., Markovitch, O., Stuart, M. C. A., Marrink, S. J., Otto, S., & Roos, W. H. (2020). Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization. Journal of the American Chemical Society, 142(32), 13709-13717. https://doi.org/10.1021/jacs.0c02635

Schroer, C. F. E., Baldauf, L., van Buren, L., Wassenaar, T. A., Melo, M. N., Koenderink, G. H., & Marrink, S. J. (2020). Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers. Proceedings of the National Academy of Sciences of the United States of America, 117(11), 5861-5872. [pnas.1914884117]. https://doi.org/10.1073/pnas.1914884117

Marrink, S. J., & Levental, I. (2020). Computational and Experimental Advances in Biomembranes: Resolving Their Complexity. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 124(45), 9975-9976. https://doi.org/10.1021/acs.jpcb.0c09401

Liu, Y., Pezeshkian, W., Barnoud, J., De Vries, A. H., & Marrink, S. J. (2020). Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. Journal of Chemical Theory and Computation, 16(8), 5313-5322. [acs.jctc.0c00429]. https://doi.org/10.1021/acs.jctc.0c00429

Liu, Y., De Vries, A. H., Barnoud, J., Pezeshkian, W., Melcr, J., & Marrink, S. J. (2020). Dual Resolution Membrane Simulations Using Virtual Sites. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 124(19), 3944-3953. https://doi.org/10.1021/acs.jpcb.0c01842

Su, J., Marrink, S. J., & Melo, M. N. (2020). Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains. Frontiers in Cell and Developmental Biology, 8, [350]. https://doi.org/10.3389/fcell.2020.00350

Vazquez-Salazar, L. I., Selle, M., de Vries, A. H., Marrink, S. J., & Souza, P. C. T. (2020). Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid-liquid extraction. Green Chemistry, 22(21), 7376-7386. https://doi.org/10.1039/d0gc01823f

Faustino, I., Abdizadeh, H., Souza, P. C. T., Jeucken, A., Stanek, W. K., Guskov, A., Slotboom, D., & Marrink, S. (2020). Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nature Communications, 11(1), [1763]. https://doi.org/10.1038/s41467-020-15554-9

Liguori, N., Croce, R., Marrink, S. J., & Thallmair, S. (2020). Molecular dynamics simulations in photosynthesis. Photosynthesis Research, 144(2), 273-295. https://doi.org/10.1007/s11120-020-00741-y

Sun, F., Schroer, C. F. E., Palacios, C. R., Xu, L., Luo, S-Z., & Marrink, S. J. (2020). Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2. PLoS Computational Biology, 16(4), [e1007777]. https://doi.org/10.1371/journal.pcbi.1007777

Kriete, B., Bondarenko, A. S., Alessandri, R., Patmanidis, I., Krasnikov, V. V., Jansen, T. L. C., Marrink, S. J., Knoester, J., & Pshenichnikov, M. S. (2020). Molecular versus excitonic disorder in individual artificial light-harvesting systems. Journal of the American Chemical Society, 142(42), 18073-18085. [jacs.0c07392]. https://doi.org/10.1021/jacs.0c07392

Bondarenko, A. S., Patmanidis, I., Alessandri, R., Souza, P. C. T., Jansen, T. L. C., de Vries, A. H., Marrink, S. J., & Knoester, J. (2020). Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates. Chemical Science, 11(42), 11514-11524. https://doi.org/10.1039/d0sc03110k

Liu, J., van der Zee, B., Alessandri, R., Sami, S., Dong, J., Nugraha, M. I., Barker, A. J., Rousseva, S., Qiu, L., Qiu, X., Klasen, N., Chiechi, R. C., Baran, D., Caironi, M., Anthopoulos, T. D., Portale, G., Havenith, R. W. A., Marrink, S. J., Hummelen, J. C., & Koster, L. J. A. (2020). N-type organic thermoelectrics: demonstration of ZT > 0.3. Nature Communications, 11(1), [5694]. https://doi.org/10.1038/s41467-020-19537-8

Buyan, A., Cox, C. D., Barnoud, J., Li, J., Chan, H. S. M., Martinac, B., Marrink, S. J., & Corry, B. (2020). Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol. Biophysical Journal, 119(8), 1683-1697. [j.bpj.2020.07.043]. https://doi.org/10.1016/j.bpj.2020.07.043

Souza, P. C. T., Thallmair, S., Conflitti, P., Ramírez-Palacios, C., Alessandri, R., Raniolo, S., Limongelli, V., & Marrink, S. J. (2020). Protein-ligand binding with the coarse-grained Martini model. Nature Communications, 11(1), [3714]. https://doi.org/10.1038/s41467-020-17437-5

Alessandri, R., Sami, S., Barnoud, J., de Vries, A. H., Marrink, S. J., & Havenith, R. W. A. (2020). Resolving Donor-Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains. Advanced Functional Materials, 30(46), [2004799]. https://doi.org/10.1002/adfm.202004799

Patmanidis, I., de Vries, A. H., Wassenaar, T. A., Wang, W., Portale, G., & Marrink, S. J. (2020). Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS. PPCP : Physical Chemistry Chemical Physics, 22(37), 21083-21093. [D0CP03282D]. https://doi.org/10.1039/d0cp03282d

Grünewald, F., Souza, P. C. T., Abdizadeh, H., Barnoud, J., de Vries, A. H., & Marrink, S. J. (2020). Titratable Martini model for constant pH simulations. The Journal of Chemical Physics, 153(2), [024118]. https://doi.org/10.1063/5.0014258

Zhou, Q., Chen, J., Luan, Y., Vainikka, P. A., Thallmair, S., Marrink, S. J., Feringa, B. L., & van Rijn, P. (2020). Unidirectional rotating molecular motors dynamically interact with adsorbed proteins to direct the fate of mesenchymal stem cells. Science Advances, 6(5), [eaay2756]. https://doi.org/10.1126/sciadv.aay2756

Draper, E. R., Dietrich, B., McAuluy, K., Brasnett, C., Abdizadeh, H., Patmanidis, I., Marrink, S., Su, H., Cui, H., Schweins, R., Seddon, A., & Adams, D. J. (2020). Using Small-Angle Scattering and Contrast Matching to Understand Molecular Packing in Low Molecular Weight Gels. Matter, 2(3), 764-778. https://doi.org/10.1016/j.matt.2019.12.028

Gopal, S. M., Pawar, A. B., Wassenaar, T. A., & Sengupta, D. (2020). Lipid-dependent conformational landscape of the ErbB2 growth factor receptor dimers. Chemistry and physics of lipids, 230, [104911]. https://doi.org/10.1016/j.chemphyslip.2020.104911

Pezeshkian, W., König, M., Marrink, S. J., & Ipsen, J. H. (2019). A Multi-Scale Approach to Membrane Remodeling Processes. Frontiers in Molecular Biosciences, 6, [59]. https://doi.org/10.3389/fmolb.2019.00059

Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, S-J., Montalban-Lopez, M., de Jong, A., Kok, J., Molenaar, D., Poolman, B., Teusink, B., & Kuipers, O. P. (2019). Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength. BMC Evolutionary Biology, 19(1), [15]. https://doi.org/10.1186/s12862-018-1331-x

Souza, P. C. T., Thallmair, S., Marrink, S. J., & Mera-Adasme, R. (2019). An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 10(24), 7740-7744. https://doi.org/10.1021/acs.jpclett.9b02868

Gholamjani Moghaddam, K., de Vries, A., Marrink, S. J., & Faraji, S. (2019). Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking. Biophysical Chemistry, 253, [106220]. https://doi.org/10.1016/j.bpc.2019.106220

Dadsena, S., Bockelmann, S., Mina, J. G. M., Hassan, D. G., Korneev, S., Razzera, G., Jahn, H., Niekamp, P., Müller, D., Schneider, M., Tafesse, F. G., Marrink, S. J., Melo, M. N., & Holthuis, J. C. M. (2019). Ceramides bind VDAC2 to trigger mitochondrial apoptosis. Nature Communications, 10(1), [1832]. https://doi.org/10.1038/s41467-019-09654-4

Marrink, S. J., Corradi, V., Souza, P. C. T., Ingólfsson, H. I., Tieleman, D. P., & Sansom, M. S. P. (2019). Computational Modeling of Realistic Cell Membranes. Chemical reviews, 119(9), 6184-6226. https://doi.org/10.1021/acs.chemrev.8b00460

Corradi, V., Sejdiu, B. I., Mesa-Galloso, H., Abdizadeh, H., Noskov, S. Y., Marrink, S. J., & Tieleman, D. P. (2019). Emerging Diversity in Lipid-Protein Interactions. Chemical reviews, 119(9), 5775-5848. https://doi.org/10.1021/acs.chemrev.8b00451

Liu, Y., Barnoud, J., & Marrink, S. J. (2019). Gangliosides Destabilize Lipid Phase Separation in Multicomponent Membranes. Biophysical Journal, 117(7), 1215-1223. https://doi.org/10.1016/j.bpj.2019.08.037

Thallmair, S., Vainikka, P. A., & Marrink, S. J. (2019). Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes. Biophysical Journal, 116(8), 1446-1455. [j.bpj.2019.03.009]. https://doi.org/10.1016/j.bpj.2019.03.009

Piskorz, T. K., Gobbo, C., Marrink, S. J., De Feyter, S., de Vries, A. H., & van Esch, J. H. (2019). Nucleation Mechanisms of Self-Assembled Physisorbed Monolayers on Graphite. Journal of Physical Chemistry C, 123(28), 17510-17520. https://doi.org/10.1021/acs.jpcc.9b01234

Alessandri, R., Souza, P. C. T., Thallmair, S., Melo, M. N., De Vries, A. H., & Marrink, S. J. (2019). Pitfalls of the Martini Model. Journal of Chemical Theory and Computation, 15(10), 5448-5460. [acs.jctc.9b00473]. https://doi.org/10.26434/chemrxiv.8113172

Newe, A., Rzeniewicz, K., Konig, M., Schroer, C. F. E., Joachim, J., Rey-Gallardo, A., Marrink, S. J., Deka, J., Parsons, M., & Ivetic, A. (2019). Serine Phosphorylation of L-Selectin Regulates ERM Binding, Clustering, and Monocyte Protrusion in Transendothelial Migration. Frontiers in Immunology, 10, [2227]. https://doi.org/10.3389/fimmu.2019.02227

Zavadlav, J., Marrink, S. J., & Praprotnik, M. (2019). SWINGER: A clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus, 9(3), [20180075]. https://doi.org/10.1098/rsfs.2018.0075

Koch, S., Exterkate, M., López, C. A., Patro, M., Marrink, S. J., & Driessen, A. J. M. (2019). Two distinct anionic phospholipid-dependent events involved in SecA-mediated protein translocation. Biochimica et Biophysica Acta - Biomembranes, 1861(11), [183035]. https://doi.org/10.1016/j.bbamem.2019.183035

Verkhnyatskaya, S. A., de Vries, A. H., Douma-de Vries, E., Sneep, R. J. L., & Walvoort, M. T. C. (2019). Direct and Regioselective Di-alpha-fucosylation on the Secondary Rim of beta-Cyclodextrin: Cover Profile. Chemistry, 25(27), 6649-6649. https://doi.org/10.1002/chem.201901257

Verkhnyatskaya, S. A., de Vries, A. H., Douma-de Vries, E., Sneep, E. J. L., & Walvoort, M. T. C. (2019). Direct and Regioselective Di-alpha-fucosylation on the Secondary Rim of beta-Cyclodextrin. Chemistry, 25(27), 6722-6727. https://doi.org/10.1002/chem.201806090

Molenaar, M. R., Jeucken, A., Wassenaar, T. A., van de Lest, C. H. A., Brouwers, J. F., & Helms, J. B. (2019). LION/web: a web-based ontology enrichment tool for lipidomic data analysis. Gigascience, 8(6), [061]. https://doi.org/10.1093/gigascience/giz061

Grunewald, F., Rossi, G., De Vries, A. H., Marrink, S. J., & Monticelli, L. (2018). A Transferable MARTINI Model of Polyethylene Oxide. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 122(29), 7436-7449. https://doi.org/10.1021/acs.jpcb.8b04760

Thallmair, S., Ingólfsson, H. I., & Marrink, S. J. (2018). Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models. The Journal of Physical Chemistry Letters, 9(18), 5527-5533. https://doi.org/10.1021/acs.jpclett.8b01877

Baoukina, S., Ingolfsson, H. I., Marrink, S. J., & Tieleman, D. P. (2018). Curvature-Induced Sorting of Lipids in Plasma Membrane Tethers. Advanced theory and simulations, 1(8), [1800034]. https://doi.org/10.1002/adts.201800034

Liu, J., Qiu, L., Alessandri, R., Qiu, X., Portale, G., Dong, J., Talsma, W., Ye, G., Sengrian, A. A., Souza, P. C. T., Loi, M. A., Chiechi, R. C., Marrink, S. J., Hummelen, J. C., & Koster, L. J. A. (2018). Enhancing Molecular n-Type Doping of Donor-Acceptor Copolymers by Tailoring Side Chains. Advanced materials, 30(7), [1704630]. https://doi.org/10.1002/adma.201704630

Zhang, M., Peyear, T., Patmanidis, I., Greathouse, D. V., Marrink, S. J., Andersen, O. S., & Ingólfsson, H. I. (2018). Fluorinated Alcohols' Effects on Lipid Bilayer Properties. Biophysical Journal, 115(4), 679-689. https://doi.org/10.1016/j.bpj.2018.07.010

Corradi, V., Mendez-Villuendas, E., Ingólfsson, H. I., Gu, R-X., Siuda, I., Melo, M. N., Moussatova, A., DeGagné, L. J., Sejdiu, B. I., Singh, G., Wassenaar, T. A., Delgado Magnero, K., Marrink, S. J., & Tieleman, D. P. (2018). Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins. ACS central science, 4(6), 709-717. https://doi.org/10.1021/acscentsci.8b00143

Bruininks, B. M., Telles De Souza, P. C., & Marrink, S. J. (2018). Microscopic View on Non-viral Mediated Transfection. Biophysical Journal, 114(3, Suppl. 1), 602a. [2989]. https://doi.org/10.1016/j.bpj.2017.11.3292

Thallmair, S., Vainikka, P. A., & Marrink, S. (2018). Molecular Dynamcis of Light-Harvesting Complex II Embedded in the Thylakoid Membrane. Biophysical Journal, 114(3, Suppl. 1), 522a. https://doi.org/10.1016/j.bpj.2017.11.2853

Sun, F., Schroer, C. F. E., Xu, L., Yin, H., Marrink, S. J., & Luo, S-Z. (2018). Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2. Biophysical Journal, 114(8), 1858-1868. https://doi.org/10.1016/j.bpj.2018.02.034

Xue, M., Cheng, L., Faustino, I., Guo, W., & Marrink, S. J. (2018). Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers. Biophysical Journal, 115(3), 494-502. https://doi.org/10.1016/j.bpj.2018.06.018

Frederix, P. W. J. M., Patmanidis, I., & Marrink, S. J. (2018). Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chemical Society Reviews, 47(10), 3470-3489. https://doi.org/10.1039/c8cs00040a

Zavadlav, J., Marrink, S. J., & Praprotnik, M. (2018). Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm. Journal of Chemical Theory and Computation, 14(3), 1754-1761. https://doi.org/10.1021/acs.jctc.7b01129

Su, J., Thomas, A. S., Grabietz, T., Landgraf, C., Volkmer, R., Marrink, S. J., Williams, C., & Melo, M. N. (2018). The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission. Biochimica et biophysica acta, 1860(6), 1292-1300. https://doi.org/10.1016/j.bbamem.2018.02.029

Souza, P. C. T., Wassenaar, T. A., Skaf, M. S., & Marrink, S. J. (2018). TLR4 Recruitment into Lipid Rafts Studied by Coarse Grained MD Simulation. Biophysical Journal, 114(3), 72a. [370]. https://doi.org/10.1016/j.bpj.2017.11.440

Friedman, R., Khalid, S., Aponte-Santamaría, C., Arutyunova, E., Becker, M., Boyd, K. J., Christensen, M., Coimbra, J. T. S., Concilio, S., Daday, C., van Eerden, F. J., Fernandes, P. A., Gräter, F., Hakobyan, D., Heuer, A., Karathanou, K., Keller, F., Lemieux, M. J., Marrink, S. J., ... Domene, C. (2018). Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. Journal of membrane biology, 251(5-6), 609-631. https://doi.org/10.1007/s00232-018-0050-y

Piskorz, T. K., de Vries, A. H., De Feyter, S., & van Esch, J. H. (2018). Mechanism of Ostwald Ripening in 2D Physisorbed Assemblies at Molecular Time and Length Scale by Molecular Dynamics Simulations. Journal of Physical Chemistry C, 122(42), 24380-24385. https://doi.org/10.1021/acs.jpcc.8b06432

Lubbe, A. S., Liu, Q., Smith, S. J., de Vries, J. W., Kistemaker, J. C. M., De Vries, A. H., Faustino, I., Meng, Z., Szymanski, W., Herrmann, A., & Feringa, B. L. (2018). Photoswitching of DNA Hybridization Using a Molecular Motor. Journal of the American Chemical Society, 140(15), 5069-5076. [jacs.7b09476]. https://doi.org/10.1021/jacs.7b09476

Jayaraman, K., Morley, A. N., Szollosi, D., Wassenaar, T. A., Sitte, H. H., & Stockner, T. (2018). Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain. PLoS Computational Biology, 14(6), [1006229]. https://doi.org/10.1371/journal.pcbi.1006229

Yildirim, A., Wassenaar, T. A., & van der Spoel, D. (2018). Statistical efficiency of methods for computing free energy of hydration. Journal of Chemical Physics, 149(14), [144111]. https://doi.org/10.1063/1.5041835

Periole, X., Huber, T., Bonito-Oliva, A., Aberg, K. C., van der Wel, P. C. A., Sakmar, T. P., & Marrink, S. J. (2018). Energetics Underlying Twist Polymorphisms in Amyloid Fibrils. The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical, 122(3), 1081–1091. https://doi.org/10.1021/acs.jpcb.7b10233

Nedergaard Pedersen, J., Wilhelmus Johannes Maria Frederix, P., Skov Pedersen, J., Marrink, S. J., & Otzen, D. (2018). Role of charge and hydrophobicity in liprotide formation: A molecular dynamics study with experimental constraints. ChemBioChem, 19, 263–271. https://doi.org/10.1002/cbic.201700496

Groves, M. R., Schroer, C. F. E., Middleton, A. J., Lunev, S., Danda, N., Ali, A. M., Marrink, S. J., & Williams, C. (2018). Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex. Biochemical and Biophysical Research Communications, 496(2), 562-567. https://doi.org/10.1016/j.bbrc.2017.12.150

Kondela, T., Gallová, J., Hauß, T., Barnoud, J., Marrink, S-J., & Kučerka, N. (2017). Alcohol Interactions with Lipid Bilayers. Molecules, 22(12), [2078]. https://doi.org/10.3390/molecules22122078

Alessandri, R., Uusitalo, J. J., De Vries, A. H., Havenith, R. W. A., & Marrink, S. J. (2017). Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations. Journal of the American Chemical Society, 139 (10), 3697–3705. [jacs.6b11717]. https://doi.org/10.1021/jacs.6b11717

Faustino, I., & Marrink, S. J. (2017). cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. Bioinformatics, 33(23), 3813-3815. [btx444]. https://doi.org/10.1093/bioinformatics/btx444

Hsu, P-C., Bruininks, B. M. H., Jefferies, D., Cesar Telles de Souza, P., Lee, J., Patel, D. S., Marrink, S. J., Qi, Y., Khalid, S., & Im, W. (2017). CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. Journal of Computational Chemistry, 38(27), 2354-2363. https://doi.org/10.1002/jcc.24895

Ingólfsson, H. I., Carpenter, T. S., Bhatia, H., Bremer, P-T., Marrink, S. J., & Lightstone, F. C. (2017). Computational Lipidomics of the Neuronal Plasma Membrane. Biophysical Journal, 113(10), 2271-2280. [j.bpj.2017.10.017]. https://doi.org/10.1016/j.bpj.2017.10.017

Liu, B., Åberg, C., van Eerden, F. J., Marrink, S., Poolman, B., & Boersma, A. J. (2017). Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding. Biophysical Journal, 112(9), 1929-1939. https://doi.org/10.1016/j.bpj.2017.04.004

Qiu, L., Liu, J., Alessandri, R., Qiu, X., Koopmans, M., Havenith, R. W. A., Marrink, S. J., Chiechi, R. C., Koster, L. J. A., & Hummelen, J. C. (2017). Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics. Journal of Materials Chemistry A, 5(40), 21234-21241. https://doi.org/10.1039/c7ta06609k

Van Eerden, F. J., Melo, M. N., Frederix, P. W. J. M., Periole, X., & Marrink, S. J. (2017). Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. Nature Communications, 8, 1-8. [15214]. https://doi.org/10.1038/ncomms15214

Gu, R-X., Ingólfsson, H. I., De Vries, A. H., Marrink, S. J., & Tieleman, D. P. (2017). Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations. Journal of Physical Chemistry B, 121(15), 3262–3275. [jpcb.6b07142]. https://doi.org/10.1021/acs.jpcb.6b07142

Melo, M. N., Arnarez, C., Sikkema, H., Kumar, N., Walko, M., Berendsen, H. J. C., Kocer, A., Marrink, S. J., & Ingólfsson, H. I. (2017). High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. Journal of the American Chemical Society, 139(7), 2664-2671. https://doi.org/10.1021/jacs.6b11091

Kanduc, M., Schlaich, A., de Vries, A. H., Jouhet, J., Marechal, E., Deme, B., Netz, R. R., & Schneck, E. (2017). Tight cohesion between glycolipid membranes results from balanced water-headgroup interactions. Nature Communications, 8, [14899]. https://doi.org/10.1038/ncomms14899

Capoferri, L., van Dijk, M., Rustenburg, A. S., Wassenaar, T. A., Kooi, D. P., Rifai, E. A., Vermeulen, N. P. E., & Geerke, D. P. (2017). eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. Journal of cheminformatics, 9, [58]. https://doi.org/10.1186/s13321-017-0243-x

Antillón, A., De Vries, A. H., Espinosa-caballero, M., Falcón-gonzález, J. M., Flores Romero, D., González–damián, J., Jiménez-montejo, F. E., León-buitimea, A., López-ortiz, M., Magaña, R., Marrink, S. J., Morales-nava, R., Periole, X., Reyes-esparza, J., Rodríguez Lozada, J., Santiago-angelino, T. M., Vargas González, M. C., Regla, I., Carrillo-tripp, M., ... Ortega-blake, I. (2016). An Amphotericin B Derivative Equally Potent to Amphotericin B and with Increased Safety. PLoS ONE, 11(9), [e0162171]. https://doi.org/10.1371/journal.pone.0162171

Gu, R-X., Ingolfsson, H. I., de Vries, A. H., Marrink, S. J., & Tieleman, D. P. (2016). Ganglioside and Protein-Ganglioside Interactions in Martini and Atomistic Molecular Dynamics Simulations. Biophysical Journal, 110(3), 254A-254A. https://doi.org/10.1016/j.bpj.2015.11.1395

Ingolfsson, H. I., Melo, M. N., Baoukina, S., Wassenaar, T. A., Periole, X., de Vries, A. H., Tieleman, D. P., & Marrink, S. J. (2016). In Silico Modeling of Biologically Complex Membranes. Biophysical Journal, 110(3), 83A-83A. https://doi.org/10.1016/j.bpj.2015.11.505

Smolyanitsky, A., Yakobson, B. I., Wassenaar, T. A., Paulechka, E., & Kroenlein, K. (2016). A MoS2-Based Capacitive Displacement Sensor for DNA Sequencing. Acs Nano, 10(9), 9009-9016. https://doi.org/10.1021/acsnano.6b05274

Pluhackova, K., Gahbauer, S., Kranz, F., Wassenaar, T. A., & Boeckmann, R. A. (2016). Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4. PLoS Computational Biology, 12(11), [1005169]. https://doi.org/10.1371/journal.pcbi.1005169

Goga, N., Melo, M. N., Rzepiela, A. J., de Vries, A., Hadar, A., Marrink, S. J., & Berendsen, H. (2015). Benchmark of Schemes for Multiscale Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 11(4), 1389-1398. https://doi.org/10.1021/ct501102b

van Eerden, F. J., de Jong, D. H., de Vries, A. H., Wassenaar, T. A., & Marrink, S. J. (2015). Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations. Biochimica et Biophysica Acta-Biomembranes, 1848(6), 1319-1330. https://doi.org/10.1016/j.bbamem.2015.02.025

Ingolfsson, H. I., Melo, M. N., Wassenaar, T. A., Periole, X., de Vries, A. H., Tieleman, D. P., & Marrink, S. J. (2015). Computational Lipidomics and the Lipid Organization of Cell Envelopes. Biophysical Journal, 108(2), 342A-342A.

Arnarez, C., Uusitalo, J. J., Masman, M. F., Ingolfsson, H. I., de Jong, D. H., Melo, M. N., Periole, X., de Vries, A. H., & Marrink, S. J. (2015). Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simblations with Implicit Solvent. Journal of Chemical Theory and Computation, 11(1), 260-275. https://doi.org/10.1021/ct500477k

Paulechka, E., Wassenaar, T., Kroenlein, K., Kazakov, A., & Smolyanitsky, A. (2016). Nucleobase-functionalized grapheme nanoribbons for accurate high-speed DNA sequencing. Nanoscale, 8, 1861-1867. https://doi.org/10.1039/C5NR07061A

Wassenaar, T. A., Ingolfsson, H. I., Boeckmann, R. A., Tieleman, D. P., & Marrink, S. J. (2015). Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations. Journal of Chemical Theory and Computation, 11(5), 2144-2155. https://doi.org/10.1021/acs.jctc.5b00209

Wassenaar, T. A., Pluhackova, K., Moussatova, A., Sengupta, D., Marrink, S. J., Tieleman, D. P., & Boeckrnann, R. A. (2015). High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. Journal of Chemical Theory and Computation, 11(5), 2278-2291. https://doi.org/10.1021/ct5010092

Zavadlav, J., Melo, M. N., Cunha, A. V., de Vries, A. H., Marrink, S. J., & Praprotnik, M. (2014). Adaptive Resolution Simulation of MARTINI Solvents. Journal of Chemical Theory and Computation, 10(6), 2591-2598. https://doi.org/10.1021/ct5001523

Negro, E., Latsuzbaia, R., de Vries, A. H., & Koper, G. J. M. (2014). Experimental and molecular dynamics characterization of dense micro emulsion systems morphology, conductivity and SAXS. Soft Matter, 10(43), 8685-8697. https://doi.org/10.1039/c4sm01763c

Haverkort, F., Stradomska, A., Vries, A. H. D., & Knoester, J. (2014). First-Principles Calculation of the Optical Properties of an Amphiphilic Cyanine Dye Aggregate. The Journal of Physical Chemistry. A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory, 118(6), 1012-1023. https://doi.org/10.1021/jp4112487

Ingólfsson, H. I., Melo, M. N., van Eerden, F. J., Arnarez, C., Lopez, C. A., Wassenaar, T. A., Periole, X., de Vries, A. H., Tieleman, D. P., & Marrink, S. J. (2014). Lipid organization of the plasma membrane. Journal of the American Chemical Society, 136(41), 14554-14559. https://doi.org/10.1021/ja507832e

Wassenaar, T. A., Pluhackova, K., Böckmann, R. A., Marrink, S. J., & Tieleman, D. P. (2014). Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. Journal of Chemical Theory and Computation, 10(2), 676-690. https://doi.org/10.1021/ct400617g

Boscia, A. L., Treece, B. W., Mohammadyani, D., Klein-Seetharaman, J., Braun, A. R., Wassenaar, T., Kloesgen, B., & Tristram-Nagle, S. (2014). X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes. Chemistry and physics of lipids, 178, 1-10. https://doi.org/10.1016/j.chemphyslip.2013.12.010

Lopez, C. A., de Vries, A. H., & Marrink, S. J. (2013). Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Scientific Reports, 3, [2071]. https://doi.org/10.1038/srep02071

Haverkort, F., Stradomska, A., de Vries, A. H., & Knoester, J. (2013). Investigating the Structure of Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics Simulations. Journal of Physical Chemistry B, 117(19), 5857-5867. https://doi.org/10.1021/jp4005696

Lopez, C. A., Sovova, Z., van Eerden, F. J., de Vries, A. H., & Marrink, S. J. (2013). Martini Force Field Parameters for Glycolipids. Journal of Chemical Theory and Computation, 9(3), 1694-1708. https://doi.org/10.1021/ct3009655

Gobbo, C., Beurroies, I., de Ridder, D., Eelkema, R., Marrink, S. J., De Feyter, S., van Esch, J. H., & de Vries, A. H. (2013). MARTINI Model for Physisorption of Organic Molecules on Graphite. Journal of Physical Chemistry C, 117(30), 15623-15631. https://doi.org/10.1021/jp402615p

de Jong, D. H., Singh, G., Bennett, W. F. D., Arnarez, C., Wassenaar, T. A., Schafer, L. V., Periole, X., Tieleman, D. P., & Marrink, S. J. (2013). Improved Parameters for the Martini Coarse-Grained Protein Force Field. Journal of Chemical Theory and Computation, 9(1), 687-697. https://doi.org/10.1021/ct300646g

Wassenaar, T. A., Ingólfsson, H. I., Priess, M., Marrink, S. J., & Schaefer, L. V. (2013). Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic-Coarse-Grained Biomolecular Simulations. Journal of Physical Chemistry B, 117(13), 3516-3530. https://doi.org/10.1021/jp311533p

Lopez, C. A., de Vries, A. H., & Marrink, S. J. (2012). Amylose folding under the influence of lipids. Carbohydrate Research, 364, 1-7. https://doi.org/10.1016/j.carres.2012.10.007

Goga, N., Rzepiela, A. J., de Vries, A. H., Marrink, S. J., & Berendsen, H. J. C. (2012). Efficient Algorithms for Langevin and DPD Dynamics. Journal of Chemical Theory and Computation, 8(10), 3637-3649. https://doi.org/10.1021/ct3000876

van Dijk, M., Wassenaar, T. A., & Bonvin, A. M. J. J. (2012). A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 8(10), 3463-3472. https://doi.org/10.1021/ct300102d

Wassenaar, T. A., Schafer, L. V., Ingolfsson, H., & Marrink, S-J. (2012). Mixing Martinis: Atomistic Simulations of MscL in a Coarse Grained Environment. Biophysical Journal, 102(3), 241a-241a. https://doi.org/10.1016/j.bpj.2011.11.1326

Wassenaar, T. A., de Vries, S., Bonvin, A. M. J. J., & Bekker, H. (2012). SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions. Journal of Chemical Theory and Computation, 8(10), 3618-3627. https://doi.org/10.1021/ct3000662

De Jong, D. H., Schafer, L. V., De Vries, A. H., Marrink, S. J., Berendsen, H. J. C., & Grubmueller, H. (2011). Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations. Journal of Computational Chemistry, 32(9), 1919-1928. https://doi.org/10.1002/jcc.21776

Schaefer, L. V., de Jong, D. H., Holt, A., Rzepiela, A. J., de Vries, A. H., Poolman, B., Killian, J. A., & Marrink, S. J. (2011). Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes. Proceedings of the National Academy of Sciences of the United States of America, 108(4), 1343-1348. https://doi.org/10.1073/pnas.1009362108

Lopez, C. A., de Vries, A. H., & Marrink, S. J. (2011). Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction. PLoS Computational Biology, 7(3), [e1002020]. https://doi.org/10.1371/journal.pcbi.1002020

Marrink, S. J., Periole, X., Tieleman, D. P., & de Vries, A. H. (2010). Comment on "On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models'' by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934. Physical Chemistry Chemical Physics, 12(9), 2254-2256. https://doi.org/10.1039/b915293h

Fuhrmans, M., Sanders, B. P., Marrink, S-J., & de Vries, A. H. (2010). Effects of bundling on the properties of the SPC water model. Theoretical Chemistry Accounts, 125(3-6), 335-344. https://doi.org/10.1007/s00214-009-0590-4

Horta, B. A. C., de Vries, A. H., & Hunenberger, P. H. (2010). Simulating the Transition between Gel and Liquid-Crystal Phases of Lipid Bilayers: Dependence of the Transition Temperature on the Hydration Level. Journal of Chemical Theory and Computation, 6(8), 2488-2500. https://doi.org/10.1021/ct100200w

Rzepiela, A. J., Schafer, L. V., Goga, N., Risselada, H. J., De Vries, A. H., & Marrink, S. J. (2010). Software News and Update Reconstruction of Atomistic Details from Coarse-Grained Structures. Journal of Computational Chemistry, 31(6), 1333-1343. https://doi.org/10.1002/jcc.21415

Lee, H., de Vries, A. H., Marrink, S-J., & Pastor, R. W. (2009). A Coarse-Grained Model for Polyethylene Oxide and Polyethylene Glycol: Conformation and Hydrodynamics. Journal of Physical Chemistry B, 113(40), 13186-13194. https://doi.org/10.1021/jp9058966

Siwko, M. E., de Vries, A. H., Mark, A. E., Kozubek, A., & Marrink, S. J. (2009). Disturb or Stabilize? A Molecular Dynamics Study of the Effects of Resorcinolic Lipids on Phospholipid Bilayers. Biophysical Journal, 96(8), 3140-3153. https://doi.org/10.1016/j.bpj.2009.01.040

Winger, M., de Vries, A. H., & van Gunsteren, W. F. (2009). Force-field dependence of the conformational properties of ,-dimethoxypolyethylene glycol. Molecular Physics, 107(13), 1313-1321. [911054506]. https://doi.org/10.1080/00268970902794826

Marrink, S. J., de Vries, A. H., & Tieleman, D. P. (2009). Lipids on the move: Simulations of membrane pores, domains, stalks and curves. Biochimica et Biophysica Acta-Biomembranes, 1788(1), 149-168. https://doi.org/10.1016/j.bbamem.2008.10.006

Hinner, M. J., Marrink, S-J., & de Vries, A. H. (2009). Location, Tilt, and Binding: A Molecular Dynamics Study of Voltage-Sensitive Dyes in Biomembranes. Journal of Physical Chemistry B, 113(48), 15807-15819. https://doi.org/10.1021/jp907981y

Lopez, C. A., Rzepiela, A. J., de Vries, A. H., Dijkhuizen, L., Huenenberger, P. H., & Marrink, S. J. (2009). Martini Coarse-Grained Force Field: Extension to Carbohydrates. Journal of Chemical Theory and Computation, 5(12), 3195-3210. https://doi.org/10.1021/ct900313w

Wassenaar, T. A., Daura, X., Padros, E., & Mark, A. E. (2009). Calcium binding to the purple membrane: A molecular dynamics study. Proteins, 74(3), 669-681. https://doi.org/10.1002/prot.22182

Marrink, S. J., de Vries, A. H., Harroun, T. A., Katsaras, J., & Wassall, S. R. (2008). Cholesterol shows preference for the interior of polyunsaturated lipid. Journal of the American Chemical Society, 130(1), 10 - 11. https://doi.org/10.1021/ja076641c

Wassenaar, T. A., Quax, W. J., & Mark, A. E. (2008). The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: A molecular dynamics study. Proteins, 70(2), 333-343. https://doi.org/10.1002/prot.21541

Baron, R., Trzesniak, D., de Vries, A. H., Elsener, A., Marrink, S. J., & van Gunsteren, W. F. (2007). Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. Chemphyschem, 8(3), 452 - 461. https://doi.org/10.1002/cphc.200600658

van den Bogaart, G., Hermans, N., Krasnikov, V., de Vries, A. H., & Poolman, B. (2007). On the decrease in lateral mobility of phospholipids by sugars. Biophysical Journal, 92(5), 1598-1605. https://doi.org/10.1529/biophysj.106.096461

Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & de Vries, A. H. (2007). The MARTINI force field: Coarse grained model for biomolecular simulations. Journal of Physical Chemistry B, 111(27), 7812-7824. https://doi.org/10.1021/jp071097f

Villa, A., Fan, H., Wassenaar, T., & Mark, A. E. (2007). How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field? Journal of Physical Chemistry B, 111(21), 6015-6025. https://doi.org/10.1021/jp068580v

Siwko, M. E., Marrink, S. J., de Vries, A. H., Arkadiusz, K., Schoot Uiterkamp, A. J. M., & Mark, A. E. (2007). Does isoprene protect plant membranes for thermal shock? A molecular dynamics study. Biochimica et Biophysica Acta-Biomembranes, 1768(2), 198-206. https://doi.org/10.1016/j.bbamem.2006.09.023

Baron, R., de Vries, A. H., Hunenberger, PH., & van Gunsteren, W. F. (2006). Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. Journal of Physical Chemistry B, 110(16), 8464-8473. https://doi.org/10.1021/jp055888y

Baron, R., de Vries, A. H., Huenenberger, P. H., & van Gunsteren, W. F. (2006). Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations. Journal of Physical Chemistry B, 110(31), 15602-15614. https://doi.org/10.1021/jp061627s

Hozoi, L., de Vries, A. H., Broer, R., de Graaf, C., & Bagus, P. S. (2006). Ni 3s-hole states in NiO by non-orthogonal configuration interaction. Chemical Physics, 331(1), 178-185. https://doi.org/10.1016/j.chemphys.2006.10.015

Wassenaar, T. A., & Mark, A. E. (2006). The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. Journal of Computational Chemistry, 27(3), 316-325. https://doi.org/10.1002/jcc.20341

de Vries, A. H., Chandrasekhar, I., van Gunsteren, W. F., Hunenberger, P. H., & Chandrasekhar, N. V. (2005). Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time: Influence of artificial periodicity, system size, and simulation time. Journal of Physical Chemistry B, 109(23), 11643-11652. https://doi.org/10.1021/jp0507952

de Vries, AH., Yefimov, S., Mark, AE., & Marrink, SJ. (2005). Molecular structure of the lecithin ripple phase. Proceedings of the National Academy of Sciences of the United States of America, 102(15), 5392-5396. https://doi.org/10.1073/pnas.0408249102

Marrink, SJ., de Vries, AH., & Mark, AE. (2004). Coarse grained model for semiquantitative lipid simulations. Journal of Physical Chemistry B, 108(2), 750-760. https://doi.org/10.1021/jp036508g

Folgering, J. H. A., Kuiper, J. M., Vries, A. H. D., Engberts, J. B. F. N., & Poolman, B. (2004). Lipid-Mediated Light Activation of a Mechanosensitive Channel of Large Conductance. Langmuir, 20(17), 6985 - 6987. https://doi.org/10.1021/la048942v

de Vries, AH., Mark, AE., & Marrink, SJ. (2004). Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail. Journal of the American Chemical Society, 126(14), 4488-4489. https://doi.org/10.1021/ja0398417

de Vries, AH., Mark, AE., & Marrink, SJ. (2004). The binary mixing behavior of phospholipids in a bilayer: A molecular dynamics study. Journal of Physical Chemistry B, 108(7), 2454-2463. https://doi.org/10.1021/jp0366926

Bekker, H., Van den Berg, JP., & Wassenaar, TA. (2004). A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints. Journal of Computational Chemistry, 25(8), 1037-1046. https://doi.org/10.1002/jcc.20050

Anezo, C., de Vries, AH., Holtje, HD., Tieleman, DP., & Marrink, SJ. (2003). Methodological issues in lipid bilayer simulations. Journal of Physical Chemistry B, 107(35), 9424-9433. https://doi.org/10.1021/jp0348981

de Vries, AH., Hozoi, L., & Broer, R. (2003). Origin of the chemical shift in X-ray absorption near-edge spectroscopy at the Mn K-Edge in manganese oxide compounds. International Journal of Quantum Chemistry, 91(1), 57-61. https://doi.org/10.1002/qua.10370

de Vries, A. H., Hozoi, L., Broer, R., & Bagus, P. S. (2002). Importance of interatomic hole screening in core-level spectroscopy of transition metal oxides: Mn 3s hole states in MnO. Physical Review B, 66(3), [035108]. https://doi.org/10.1103/PhysRevB.66.035108

van Duijnen, P. T., de Vries, A. H., Swart, M., & Grozema, F. C. (2002). Polarizabilities in the condensed phase and the local fields problem: A direct reaction field formulation. Journal of Chemical Physics, 117(18), 8442 - 8453. https://doi.org/10.1063/1.1512278

Hozoi, L., de Vries, A. H., van Oosten, A. B., Broer-Braam, H. B., Cabrero, J., & Graaf, de, C. (2002). Theoretical characterization of the ground and optically excited states of alpha '-NaV2O5. Physical Review Letters, 89(7), [076407]. https://doi.org/10.1103/physrevlett.89.076407

Hozoi, L., de Vries, A. H., & Broer-Braam, H. B. (2001). X-ray spectroscopy at the MnK edge in LaMnO3: An ab initio study. Physical Review B, 64(16), [165104]. https://doi.org/10.1103/PhysRevB.64.165104

de Vries, A. H., Sherwood, P., Collins, S. J., Rigby, A. M., Rigutto, M., & Kramer, G. J. (1999). Zeolite structure and reactivity by combined quantum-chemical- classical calculations. Journal of Physical Chemistry B, 103(29), 6133 - 6141. https://doi.org/10.1021/jp9913012

Sinclair, P. E., De Vries, A., Sherwood, P., Catlow, C. R. A., & Van Santen, R. A. (1998). Quantum-chemical studies of alkene chemisorption in chabazite: A comparison of cluster and embedded-cluster models. Journal of the Chemical Society - Faraday Transactions, 94(22), 3401-3408. https://doi.org/10.1039/a805616a

Sherwood, P., De Vries, A. H., Collins, S. J., Greatbanks, S. P., Burton, N. A., Vincent, M. A., & Hillier, I. H. (1997). Computer simulation of zeolite structure and reactivity using embedded cluster methods. Faraday Discussions, 106, 79-92. https://doi.org/10.1039/a701790a

deVries, AH., vanDuijnen, PT., Zijlstra, RWJ., & Swart, M. (1997). Thole's interacting polarizability model in computational chemistry practice. Journal of Electron Spectroscopy and Related Phenomena, 86(1-3), 49-55.

Duijnen , van, P. T., & de Vries, A. H. (1996). Direct reaction field force field: A consistent way to connect and combine quantum-chemical and classical descriptions of molecules. International Journal of Quantum Chemistry, 60(6), 1111-1132.

Zijlstra, R. W. J., van Duijnen, P. T., & de Vries, A. (1996). Polarization of the excited states of twisted ethylene in a non-symmetrical environment. Chemical Physics, 204(2-3), 439-446.

De Vries, A. H., & Van Duijnen, P. T. (1996). Solvatochromism of the π* ← n transition of acetone by combined quantum mechanical—classical mechanical calculations. International Journal of Quantum Chemistry, 57(6), 1067-1076. https://doi.org/10.1002/(sici)1097-461x(1996)57:6<1067::aid-qua5>3.0.co;2-r

De Vries, A. H., Van Duijnen, P. T., Juffer, A. H., Rullmann, J. A. C., Dijkman, J. P., Merenga, H., & Thole, B. T. (1995). Erratum: Implementation of reaction field methods in quantum chemistry computer codes (Vol 16, Pg 37, 1995). Journal of Computational Chemistry, 16(11), 1445-1446. https://doi.org/10.1002/jcc.540161113

De Vries, A. H., Van Duijnen, P. T., Juffer, A. H., Rullmann, J. A. C., Dijkman, J. P., MERENGA, H., & Thole, B. T. (1995). Implementation of reaction field methods in quantum chemistry computer codes. Journal of Computational Chemistry, 16(1), 37-55. https://doi.org/10.1002/jcc.540160105

Van Duijnen, P. T., & De Vries, A. H. (1995). Utopia dielectrica. International Journal of Quantum Chemistry, 56(S29), 523-531. https://doi.org/10.1002/qua.560560855

DEVRIES, AH., VANDUIJNEN, PT., & JUFFER, AH. (1993). SUCCESS AND PITFALLS OF THE DIELECTRIC CONTINUUM MODEL IN QUANTUM-CHEMICAL CALCULATIONS. International Journal of Quantum Chemistry, 451-466.

de Vries, A. H., & van Duijnen, P. T. (1992). Theoretical calculation of tautomer equilibria of 4-substituted imidazoles in the gas phase and in solution. Biophysical Chemistry, 43(2), 139-147. https://doi.org/10.1016/0301-4622(92)80028-4