Siewert Jan Marrink - Publications

University of Groningen, Groningen, Netherlands 

221 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Machado N, Bruininks BMH, Singh P, Dos Santos L, Dal Pizzol C, Dieamant GC, Kruger O, Martin AA, Marrink SJ, Souza PCT, Favero PP. Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes. Nanoscale. PMID 34913938 DOI: 10.1039/d1nr04610a  1
2021 Dong J, Sami S, Balazs DM, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith RWA, Hummelen JC, Loi MA, Portale G. Fullerene derivatives with oligoethylene-glycol side chains: an investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry. C. 9: 16217-16225. PMID 34912563 DOI: 10.1039/d1tc02753k  1
2021 Ramírez-Palacios C, Wijma HJ, Thallmair S, Marrink SJ, Janssen DB. Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. PMID 34653331 DOI: 10.1021/acs.jcim.1c00617  1
2021 Patmanidis I, Alessandri R, de Vries AH, Marrink SJ. Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields. Molecules (Basel, Switzerland). 26. PMID 34641613 DOI: 10.3390/molecules26196069  1
2021 Stehantsev P, Stetsenko A, Nemchinova M, Aduri NG, Marrink SJ, Gati C, Guskov A. A structural view onto disease-linked mutations in the human neutral amino acid exchanger ASCT1. Computational and Structural Biotechnology Journal. 19: 5246-5254. PMID 34630942 DOI: 10.1016/j.csbj.2021.09.015  1
2021 Meng Q, Ramírez-Palacios C, Capra N, Hooghwinkel ME, Thallmair S, Rozeboom HJ, Thunnissen AWH, Wijma HJ, Marrink SJ, Janssen DB. Computational Redesign of an ω-Transaminase from for Asymmetric Synthesis of Enantiopure Bulky Amines. Acs Catalysis. 11: 10733-10747. PMID 34504735 DOI: 10.1021/acscatal.1c02053  1
2021 Thallmair S, Javanainen M, Fábián B, Martinez-Seara H, Marrink SJ. Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations. The Journal of Physical Chemistry. B. 125: 9537-9546. PMID 34398598 DOI: 10.1021/acs.jpcb.1c03665  1
2021 Liu Y, de Vries AH, Pezeshkian W, Marrink SJ. Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 34165988 DOI: 10.1021/acs.jctc.1c00151  1
2021 Kjølbye LR, De Maria L, Wassenaar TA, Abdizadeh H, Marrink SJ, Ferkinghoff-Borg J, Schiøtt B. General Protocol for Constructing Molecular Models of Nanodiscs. Journal of Chemical Information and Modeling. PMID 34048229 DOI: 10.1021/acs.jcim.1c00157  1
2021 Kobauri P, Szymanski W, Cao F, Thallmair S, Marrink SJ, Witte MD, Dekker FJ, Feringa BL. Biaryl sulfonamides as azosteres for photopharmacology. Chemical Communications (Cambridge, England). 57: 4126-4129. PMID 33908493 DOI: 10.1039/d1cc00950h  1
2021 Souza PCT, Limongelli V, Wu S, Marrink SJ, Monticelli L. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Frontiers in Molecular Biosciences. 8: 657222. PMID 33855050 DOI: 10.3389/fmolb.2021.657222  1
2021 Souza PCT, Alessandri R, Barnoud J, Thallmair S, Faustino I, Grünewald F, Patmanidis I, Abdizadeh H, Bruininks BMH, Wassenaar TA, Kroon PC, Melcr J, Nieto V, Corradi V, Khan HM, ... ... Marrink SJ, et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods. PMID 33782607 DOI: 10.1038/s41592-021-01098-3  1
2020 Bondarenko AS, Patmanidis I, Alessandri R, Souza PCT, Jansen TLC, de Vries AH, Marrink SJ, Knoester J. Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates. Chemical Science. 11: 11514-11524. PMID 34094396 DOI: 10.1039/d0sc03110k  1
2020 Marrink SJ, Levental I. Computational and Experimental Advances in Biomembranes: Resolving Their Complexity. The Journal of Physical Chemistry. B. 124: 9975-9976. PMID 33176427 DOI: 10.1021/acs.jpcb.0c09401  0.01
2020 Liu J, van der Zee B, Alessandri R, Sami S, Dong J, Nugraha MI, Barker AJ, Rousseva S, Qiu L, Qiu X, Klasen N, Chiechi RC, Baran D, Caironi M, Anthopoulos TD, ... ... Marrink SJ, et al. N-type organic thermoelectrics: demonstration of ZT > 0.3. Nature Communications. 11: 5694. PMID 33173050 DOI: 10.1038/s41467-020-19537-8  1
2020 Kriete B, Bondarenko AS, Alessandri R, Patmanidis I, Krasnikov VV, Jansen TLC, Marrink SJ, Knoester J, Pshenichnikov MS. Molecular versus Excitonic Disorder in Individual Artificial Light-Harvesting Systems. Journal of the American Chemical Society. PMID 32985187 DOI: 10.1021/jacs.0c07392  1
2020 Buyan A, Cox CD, Barnoud J, Li J, Chan HSM, Martinac B, Marrink SJ, Corry B. Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol. Biophysical Journal. PMID 32949489 DOI: 10.1016/J.Bpj.2020.07.043  1
2020 Maity S, Ottelé J, Santiago GM, Frederix PWJM, Kroon P, Markovitch O, Stuart MCA, Marrink SJ, Otto S, Roos WH. Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization. Journal of the American Chemical Society. 142: 13709-13717. PMID 32786814 DOI: 10.1021/Jacs.0C02635  1
2020 Liu Y, Pezeshkian W, Barnoud J, De Vries AH, Marrink SJ. Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. Journal of Chemical Theory and Computation. PMID 32569465 DOI: 10.1021/acs.jctc.0c00429  1
2020 Su J, Marrink SJ, Melo MN. Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains. Frontiers in Cell and Developmental Biology. 8: 350. PMID 32509780 DOI: 10.3389/fcell.2020.00350  1
2020 Liu Y, De Vries AH, Barnoud J, Pezeshkian W, Melcr J, Marrink SJ. Dual Resolution Membrane Simulations Using Virtual Sites. The Journal of Physical Chemistry. B. PMID 32314586 DOI: 10.1021/acs.jpcb.0c01842  1
2020 Liguori N, Croce R, Marrink SJ, Thallmair S. Molecular dynamics simulations in photosynthesis. Photosynthesis Research. PMID 32297102 DOI: 10.1007/S11120-020-00741-Y  1
2020 Sun F, Schroer CFE, Palacios CR, Xu L, Luo SZ, Marrink SJ. Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2. Plos Computational Biology. 16: e1007777. PMID 32271757 DOI: 10.1371/Journal.Pcbi.1007777  1
2020 Schroer CFE, Baldauf L, van Buren L, Wassenaar TA, Melo MN, Koenderink GH, Marrink SJ. Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers. Proceedings of the National Academy of Sciences of the United States of America. PMID 32123101 DOI: 10.1073/pnas.1914884117  1
2020 Khan HM, Telles de Souza PC, Thallmair S, Barnoud J, De Vries AH, Marrink SJ, Reuter N. Capturing choline-aromatics cation-π interactions in the MARTINI force field. Journal of Chemical Theory and Computation. PMID 32096995 DOI: 10.1021/Acs.Jctc.9B01194  1
2020 Zhou Q, Chen J, Luan Y, Vainikka PA, Thallmair S, Marrink SJ, Feringa BL, van Rijn P. Unidirectional rotating molecular motors dynamically interact with adsorbed proteins to direct the fate of mesenchymal stem cells. Science Advances. 6: eaay2756. PMID 32064345 DOI: 10.1126/sciadv.aay2756  1
2019 Newe A, Rzeniewicz K, König M, Schroer CFE, Joachim J, Rey-Gallardo A, Marrink SJ, Deka J, Parsons M, Ivetic A. Serine Phosphorylation of L-Selectin Regulates ERM Binding, Clustering, and Monocyte Protrusion in Transendothelial Migration. Frontiers in Immunology. 10: 2227. PMID 31608057 DOI: 10.3389/fimmu.2019.02227  1
2019 Liu Y, Barnoud J, Marrink SJ. Gangliosides Destabilize Lipid Phase Separation in Multicomponent Membranes. Biophysical Journal. PMID 31542224 DOI: 10.1016/j.bpj.2019.08.037  1
2019 Koch S, Exterkate M, López CA, Patro M, Marrink SJ, Driessen AJM. Two distinct anionic phospholipid-dependent events involved in SecA-mediated protein translocation. Biochimica Et Biophysica Acta. Biomembranes. 183035. PMID 31394098 DOI: 10.1016/J.Bbamem.2019.183035  1
2019 Moghaddam KG, de Vries AH, Marrink SJ, Faraji S. Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking. Biophysical Chemistry. 253: 106220. PMID 31302375 DOI: 10.1016/J.Bpc.2019.106220  1
2019 Dadsena S, Bockelmann S, Mina JGM, Hassan DG, Korneev S, Razzera G, Jahn H, Niekamp P, Müller D, Schneider M, Tafesse FG, Marrink SJ, Melo MN, Holthuis JCM. Ceramides bind VDAC2 to trigger mitochondrial apoptosis. Nature Communications. 10: 1832. PMID 31015432 DOI: 10.1038/s41467-019-09654-4  1
2019 Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chemical Reviews. PMID 30758191 DOI: 10.1021/Acs.Chemrev.8B00451  1
2019 Price CE, Branco Dos Santos F, Hesseling A, Uusitalo JJ, Bachmann H, Benavente V, Goel A, Berkhout J, Bruggeman FJ, Marrink SJ, Montalban-Lopez M, de Jong A, Kok J, Molenaar D, Poolman B, et al. Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength. Bmc Evolutionary Biology. 19: 15. PMID 30630406 DOI: 10.1186/S12862-018-1331-X  1
2019 Marrink SJ, Corradi V, Souza PCT, Ingólfsson HI, Tieleman DP, Sansom MSP. Computational Modeling of Realistic Cell Membranes. Chemical Reviews. PMID 30623647 DOI: 10.1021/Acs.Chemrev.8B00460  1
2019 Jefferys EE, Bruininks B, Souza PCT, Marrink S, Sansom MS. Towards Molecular Simulations of Juxtaposed Biomembranes Biophysical Journal. 116: 176a. DOI: 10.1016/J.Bpj.2018.11.980  0.01
2019 Buyan A, Cox CD, Barnoud J, Martinac B, Marrink S, Corry B. Understanding Piezo1's Relationship with Lipids Biophysical Journal. 116: 459a. DOI: 10.1016/J.Bpj.2018.11.2481  0.01
2018 Friedman R, Khalid S, Aponte-Santamaría C, Arutyunova E, Becker M, Boyd KJ, Christensen M, Coimbra JTS, Concilio S, Daday C, van Eerden FJ, Fernandes PA, Gräter F, Hakobyan D, Heuer A, ... ... Marrink SJ, et al. Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. The Journal of Membrane Biology. PMID 30350011 DOI: 10.1007/S00232-018-0050-Y  1
2018 Zhang M, Peyear T, Patmanidis I, Greathouse DV, Marrink SJ, Andersen OS, Ingólfsson HI. Fluorinated Alcohols' Effects on Lipid Bilayer Properties. Biophysical Journal. PMID 30077334 DOI: 10.1016/J.Bpj.2018.07.010  1
2018 Xue M, Cheng L, Faustino I, Guo W, Marrink SJ. Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers. Biophysical Journal. PMID 29980293 DOI: 10.1016/j.bpj.2018.06.018  1
2018 Corradi V, Mendez-Villuendas E, Ingólfsson HI, Gu RX, Siuda I, Melo MN, Moussatova A, DeGagné LJ, Sejdiu BI, Singh G, Wassenaar TA, Delgado Magnero K, Marrink SJ, Tieleman DP. Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins. Acs Central Science. 4: 709-717. PMID 29974066 DOI: 10.1021/acscentsci.8b00143  1
2018 Grunewald F, Rossi G, de Vries AH, Marrink SJ, Monticelli L. Transferable MARTINI Model of Poly(ethylene Oxide). The Journal of Physical Chemistry. B. PMID 29966087 DOI: 10.1021/acs.jpcb.8b04760  1
2018 Sun F, Schroer CFE, Xu L, Yin H, Marrink SJ, Luo SZ. Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2. Biophysical Journal. 114: 1858-1868. PMID 29694864 DOI: 10.1016/J.Bpj.2018.02.034  1
2018 Su J, Thomas AS, Grabietz T, Landgraf C, Volkmer R, Marrink SJ, Williams C, Melo MN. The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission. Biochimica Et Biophysica Acta. PMID 29501607 DOI: 10.1016/j.bbamem.2018.02.029  1
2018 Liu J, Qiu L, Alessandri R, Qiu X, Portale G, Dong J, Talsma W, Ye G, Sengrian AA, Souza PCT, Loi MA, Chiechi RC, Marrink SJ, Hummelen JC, Koster LJA. Enhancing Molecular n-Type Doping of Donor-Acceptor Copolymers by Tailoring Side Chains. Advanced Materials (Deerfield Beach, Fla.). PMID 29325212 DOI: 10.1002/Adma.201704630  1
2018 Nedergaard Pedersen J, Frederix PWJM, Skov Pedersen J, Marrink SJ, Otzen DE. Role of Charge and Hydrophobicity in Liprotide Formation: A Molecular Dynamics Study with Experimental Constraints. Chembiochem : a European Journal of Chemical Biology. 19: 263-271. PMID 29156084 DOI: 10.1002/cbic.201700496  1
2018 Kroon PC, Wassenaar TA, Barnoud J, Marrink S. New Automated and High-throughput Tools for the Martini Forcefield Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.3648  1
2017 Swier LJYM, Monjas L, Reeßing F, Oudshoorn RC, Aisyah A, Primke T, Bakker MM, Olst EV, Ritschel T, Faustino I, Marrink SJ, Hirsch AKH, Slotboom DJ. Insight into the complete substrate-binding pocket of ThiT by chemical and genetic mutations. Medchemcomm. 8: 1121-1130. PMID 30108823 DOI: 10.1039/C7Md00079K  1
2017 Groves MR, Schroer CFE, Middleton AJ, Lunev S, Danda N, Ali AM, Marrink SJ, Williams C. Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex. Biochemical and Biophysical Research Communications. PMID 29288668 DOI: 10.1016/j.bbrc.2017.12.150  1
2017 Periole X, Huber T, Bonito-Oliva A, Aberg KC, van der Wel PCA, Sakmar TP, Marrink SJ. Energetics Underlying Twist Polymorphisms in Amyloid Fibrils. The Journal of Physical Chemistry. B. PMID 29254334 DOI: 10.1021/Acs.Jpcb.7B10233  1
2017 Ingólfsson HI, Carpenter TS, Bhatia H, Bremer PT, Marrink SJ, Lightstone FC. Computational Lipidomics of the Neuronal Plasma Membrane. Biophysical Journal. PMID 29113676 DOI: 10.1016/J.Bpj.2017.10.017  1
2017 Faustino I, Marrink SJ. cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. Bioinformatics (Oxford, England). PMID 29036584 DOI: 10.1093/bioinformatics/btx444  1
2017 Hsu PC, Bruininks BMH, Jefferies D, Cesar Telles de Souza P, Lee J, Patel DS, Marrink SJ, Qi Y, Khalid S, Im W. CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. Journal of Computational Chemistry. PMID 28776689 DOI: 10.1002/Jcc.24895  1
2017 Frederix PWJM, Idé J, Altay Y, Schaeffer G, Surin M, Beljonne D, Bondarenko AS, Jansen TLC, Otto S, Marrink SJ. Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles. Acs Nano. PMID 28723067 DOI: 10.1021/Acsnano.7B02211  1
2017 Liu B, Åberg C, van Eerden FJ, Marrink SJ, Poolman B, Boersma AJ. Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding. Biophysical Journal. 112: 1929-1939. PMID 28494963 DOI: 10.1016/j.bpj.2017.04.004  1
2017 Maingi V, Burns JR, Uusitalo JJ, Howorka S, Marrink SJ, Sansom MS. Stability and dynamics of membrane-spanning DNA nanopores. Nature Communications. 8: 14784. PMID 28317903 DOI: 10.1038/Ncomms14784  1
2017 Melo MN, Arnarez C, Sikkema H, Kumar N, Walko M, Berendsen HJ, Kocer A, Marrink SJ, Ingólfsson HI. High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating. Journal of the American Chemical Society. PMID 28122455 DOI: 10.1021/Jacs.6B11091  1
2016 Venable RM, Ingólfsson HI, Lerner MG, Perrin BS, Camley BA, Marrink SJ, Brown FL, Pastor RW. Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions. The Journal of Physical Chemistry. B. PMID 27966982 DOI: 10.1021/Acs.Jpcb.6B09111  1
2016 Guskov A, Jensen S, Faustino I, Marrink SJ, Slotboom DJ. Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk. Nature Communications. 7: 13420. PMID 27830699 DOI: 10.1038/ncomms13420  1
2016 Antillón A, de Vries AH, Espinosa-Caballero M, Falcón-González JM, Flores Romero D, González-Damián J, Jiménez-Montejo FE, León-Buitimea A, López-Ortiz M, Magaña R, Marrink SJ, Morales-Nava R, Periole X, Reyes-Esparza J, Rodríguez Lozada J, et al. An Amphotericin B Derivative Equally Potent to Amphotericin B and with Increased Safety. Plos One. 11: e0162171. PMID 27683101 DOI: 10.1371/journal.pone.0162171  1
2016 van Eerden FJ, van den Berg T, Frederix PW, de Jong DH, Periole X, Marrink SJ. Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane. The Journal of Physical Chemistry. B. PMID 27624992 DOI: 10.1021/acs.jpcb.6b06865  1
2016 Gu RX, Ingólfsson HI, De Vries AH, Marrink SJ, Tieleman DP. Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 27610460 DOI: 10.1021/acs.jpcb.6b07142  1
2016 Smeets CJ, Zmorzyńska J, Melo MN, Stargardt A, Dooley C, Bakalkin G, McLaughlin J, Sinke RJ, Marrink SJ, Reits E, Verbeek DS. Altered secondary structure of Dynorphin A associates with loss of opioid signalling and NMDA-mediated excitotoxicity in SCA23. Human Molecular Genetics. PMID 27260403 DOI: 10.1093/Hmg/Ddw130  1
2016 Zavadlav J, Podgornik R, Melo MN, Marrink SJ, Praprotnik M. Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution European Physical Journal-Special Topics. 225: 1595-1607. DOI: 10.1140/Epjst/E2016-60117-8  1
2016 Faustino I, Marrink S. Effects of H2A Histone Variants on DNA Sequence and Nucleosome Structure using Coarse Grain Simulations Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.3002  1
2016 Maingi V, Uusitalo JJ, Lelimousin M, Howorka S, Marrink SJ, Sansom MSP. DNA-Origami Nanotubes and their Interaction with Membranes : Insights through Multiscale Molecular Dynamics Simulations Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.2195  1
2015 Uytterhoeven V, Lauwers E, Maes I, Miskiewicz K, Melo MN, Swerts J, Kuenen S, Wittocx R, Corthout N, Marrink SJ, Munck S, Verstreken P. Hsc70-4 Deforms Membranes to Promote Synaptic Protein Turnover by Endosomal Microautophagy. Neuron. 88: 735-48. PMID 26590345 DOI: 10.1016/J.Neuron.2015.10.012  1
2015 Qi Y, Ingólfsson HI, Cheng X, Lee J, Marrink SJ, Im W. CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field. Journal of Chemical Theory and Computation. 11: 4486-4494. PMID 26575938 DOI: 10.1021/Acs.Jctc.5B00513  1
2015 Uusitalo JJ, Ingólfsson HI, Akhshi P, Tieleman DP, Marrink SJ. Martini Coarse-Grained Force Field: Extension to DNA. Journal of Chemical Theory and Computation. 11: 3932-45. PMID 26574472 DOI: 10.1021/acs.jctc.5b00286  1
2015 Wassenaar TA, Pluhackova K, Moussatova A, Sengupta D, Marrink SJ, Tieleman DP, Böckmann RA. High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. Journal of Chemical Theory and Computation. 11: 2278-91. PMID 26574426 DOI: 10.1021/ct5010092  1
2015 Wassenaar TA, Ingólfsson HI, Böckmann RA, Tieleman DP, Marrink SJ. Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations. Journal of Chemical Theory and Computation. 11: 2144-55. PMID 26574417 DOI: 10.1021/acs.jctc.5b00209  1
2015 Arnarez C, Uusitalo JJ, Masman MF, Ingólfsson HI, de Jong DH, Melo MN, Periole X, de Vries AH, Marrink SJ. Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent. Journal of Chemical Theory and Computation. 11: 260-75. PMID 26574224 DOI: 10.1021/ct500477k  1
2015 Liguori N, Periole X, Marrink SJ, Croce R. From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII). Scientific Reports. 5: 15661. PMID 26493782 DOI: 10.1038/Srep15661  1
2015 van der Velde JH, Uusitalo JJ, Ugen LJ, Warszawik EM, Herrmann A, Marrink SJ, Cordes T. Intramolecular photostabilization via triplet-state quenching: design principles to make organic fluorophores "self-healing". Faraday Discussions. PMID 26449795 DOI: 10.1039/C5Fd00114E  1
2015 de Jong DH, Liguori N, van den Berg T, Arnarez C, Periole X, Marrink SJ. Correction to "Atomistic and Coarse Grain Topologies for the Cofactors Associated with the PhotoSystem II Core Complex". The Journal of Physical Chemistry. B. 119: 10372. PMID 26230361 DOI: 10.1021/Acs.Jpcb.5B06925  1
2015 de Jong DH, Liguori N, van den Berg T, Arnarez C, Periole X, Marrink SJ. Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex. The Journal of Physical Chemistry. B. 119: 7791-803. PMID 26053327 DOI: 10.1021/Acs.Jpcb.5B00809  1
2015 van Eerden FJ, de Jong DH, de Vries AH, Wassenaar TA, Marrink SJ. Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations. Biochimica Et Biophysica Acta. 1848: 1319-30. PMID 25749153 DOI: 10.1016/j.bbamem.2015.02.025  1
2015 Wijma HJ, Floor RJ, Bjelic S, Marrink SJ, Baker D, Janssen DB. Enantioselective enzymes by computational design and in silico screening. Angewandte Chemie (International Ed. in English). 54: 3726-30. PMID 25651000 DOI: 10.1002/Anie.201411415  1
2015 Heberling MM, Masman MF, Bartsch S, Wybenga GG, Dijkstra BW, Marrink SJ, Janssen DB. Ironing out their differences: dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase. Acs Chemical Biology. 10: 989-97. PMID 25494407 DOI: 10.1021/Cb500794H  1
2015 López CA, Bellesia G, Redondo A, Langan P, Chundawat SP, Dale BE, Marrink SJ, Gnanakaran S. MARTINI coarse-grained model for crystalline cellulose microfibers. The Journal of Physical Chemistry. B. 119: 465-73. PMID 25417548 DOI: 10.1021/Jp5105938  1
2015 Goga N, Melo MN, Rzepiela AJ, De Vries AH, Hadar A, Marrink SJ, Berendsen HJC. Benchmark of schemes for multiscale molecular dynamics simulations Journal of Chemical Theory and Computation. 11: 1389-1398. DOI: 10.1021/ct501102b  1
2015 Wassenaar TA, Pluhackova K, Moussatova A, Sengupta D, Marrink SJ, Tieleman DP, Böckmann RA. High-throughput simulations of dimer and trimer assembly of membrane proteins. The DAFT approach Journal of Chemical Theory and Computation. 11: 2278-2291. DOI: 10.1021/ct5010092  1
2014 Zavadlav J, Melo MN, Cunha AV, de Vries AH, Marrink SJ, Praprotnik M. Adaptive Resolution Simulation of MARTINI Solvents. Journal of Chemical Theory and Computation. 10: 2591-8. PMID 26580779 DOI: 10.1021/ct5001523  1
2014 Wassenaar TA, Pluhackova K, Böckmann RA, Marrink SJ, Tieleman DP. Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. Journal of Chemical Theory and Computation. 10: 676-90. PMID 26580045 DOI: 10.1021/ct400617g  1
2014 Konijnenberg A, Yilmaz D, Ingólfsson HI, Dimitrova A, Marrink SJ, Li Z, Vénien-Bryan C, Sobott F, Koçer A. Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 111: 17170-5. PMID 25404294 DOI: 10.1073/pnas.1413118111  1
2014 Moiset G, López CA, Bartelds R, Syga L, Rijpkema E, Cukkemane A, Baldus M, Poolman B, Marrink SJ. Disaccharides impact the lateral organization of lipid membranes. Journal of the American Chemical Society. 136: 16167-75. PMID 25316578 DOI: 10.1021/Ja505476C  1
2014 Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ. The power of coarse graining in biomolecular simulations. Wiley Interdisciplinary Reviews. Computational Molecular Science. 4: 225-248. PMID 25309628 DOI: 10.1002/wcms.1169  1
2014 Barnoud J, Rossi G, Marrink SJ, Monticelli L. Hydrophobic compounds reshape membrane domains. Plos Computational Biology. 10: e1003873. PMID 25299598 DOI: 10.1371/journal.pcbi.1003873  1
2014 Ingólfsson HI, Melo MN, van Eerden FJ, Arnarez C, Lopez CA, Wassenaar TA, Periole X, de Vries AH, Tieleman DP, Marrink SJ. Lipid organization of the plasma membrane. Journal of the American Chemical Society. 136: 14554-9. PMID 25229711 DOI: 10.1021/ja507832e  1
2014 Mili?evi? Z, Marrink SJ, Smith AS, Smith DM. Establishing conditions for simulating hydrophobic solutes in electric fields by molecular dynamics: effects of the long-range van der Waals treatment on the apparent particle mobility. Journal of Molecular Modeling. 20: 2359. PMID 25102936 DOI: 10.1007/S00894-014-2359-5  1
2014 Floor RJ, Wijma HJ, Colpa DI, Ramos-Silva A, Jekel PA, Szyma?ski W, Feringa BL, Marrink SJ, Janssen DB. Computational library design for increasing haloalkane dehalogenase stability. Chembiochem : a European Journal of Chemical Biology. 15: 1660-72. PMID 24976371 DOI: 10.1002/cbic.201402128  1
2014 Mukherjee N, Jose MD, Birkner JP, Walko M, Ingólfsson HI, Dimitrova A, Arnarez C, Marrink SJ, Koçer A. The activation mode of the mechanosensitive ion channel, MscL, by lysophosphatidylcholine differs from tension-induced gating. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 28: 4292-302. PMID 24958207 DOI: 10.1096/fj.14-251579  1
2014 Ingólfsson HI, Thakur P, Herold KF, Hobart EA, Ramsey NB, Periole X, de Jong DH, Zwama M, Yilmaz D, Hall K, Maretzky T, Hemmings HC, Blobel C, Marrink SJ, Koçer A, et al. Phytochemicals perturb membranes and promiscuously alter protein function. Acs Chemical Biology. 9: 1788-98. PMID 24901212 DOI: 10.1021/Cb500086E  1
2014 Kozlov MM, Campelo F, Liska N, Chernomordik LV, Marrink SJ, McMahon HT. Mechanisms shaping cell membranes. Current Opinion in Cell Biology. 29: 53-60. PMID 24747171 DOI: 10.1016/  1
2014 Campelo F, Arnarez C, Marrink SJ, Kozlov MM. Helfrich model of membrane bending: from Gibbs theory of liquid interfaces to membranes as thick anisotropic elastic layers. Advances in Colloid and Interface Science. 208: 25-33. PMID 24560031 DOI: 10.1016/j.cis.2014.01.018  1
2014 Wijma HJ, Floor RJ, Jekel PA, Baker D, Marrink SJ, Janssen DB. Computationally designed libraries for rapid enzyme stabilization Protein Engineering, Design and Selection. 27: 49-58. PMID 24402331 DOI: 10.1093/Protein/Gzt061  1
2014 Akhshi P, Uusitalo J, Ingolfsson H, Marrink S, Tieleman DP. Development of Coarse-Grained Martini Model for Nucleic Acid Structures Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.3896  1
2014 Ingólfsson HI, Arnarez C, Kumar N, Walko M, Berendsen HJC, Koçer A, Marrink SJ. Membrane Dependence of the Mechanosensitive Channel of Large Conductance Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.284  1
2014 Arnarez C, Marrink S, Periole X. Cardiolipins at the Interface of Supercomplexes in the Respiratory Chain Biophysical Journal. 106: 27. DOI: 10.1016/J.Bpj.2013.11.204  1
2014 Eerden FJv, Jong DHd, Periole X, Marrink S. Simulation of Photosystem Ii Dynamics in the Thylakoid Membrane Biophysical Journal. 106: 1-1. DOI: 10.1016/J.Bpj.2013.11.1025  1
2013 de Jong DH, Singh G, Bennett WF, Arnarez C, Wassenaar TA, Schäfer LV, Periole X, Tieleman DP, Marrink SJ. Improved Parameters for the Martini Coarse-Grained Protein Force Field. Journal of Chemical Theory and Computation. 9: 687-97. PMID 26589065 DOI: 10.1021/ct300646g  1
2013 López CA, Sovova Z, van Eerden FJ, de Vries AH, Marrink SJ. Martini Force Field Parameters for Glycolipids. Journal of Chemical Theory and Computation. 9: 1694-708. PMID 26587629 DOI: 10.1021/ct3009655  1
2013 Bulacu M, Goga N, Zhao W, Rossi G, Monticelli L, Periole X, Tieleman DP, Marrink SJ. Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 9: 3282-92. PMID 26584087 DOI: 10.1021/ct400219n  1
2013 Baaden M, Marrink SJ. Coarse-grain modelling of protein-protein interactions. Current Opinion in Structural Biology. 23: 878-86. PMID 24172141 DOI: 10.1016/J.Sbi.2013.09.004  0.01
2013 Hu M, de Jong DH, Marrink SJ, Deserno M. Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model. Faraday Discussions. 161: 365-82; discussion 4. PMID 23805750 DOI: 10.1039/C2Fd20087B  1
2013 de Jong DH, Lopez CA, Marrink SJ. Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Faraday Discussions. 161: 347-63; discussion 4. PMID 23805749 DOI: 10.1039/C2FD20086D  1
2013 López CA, de Vries AH, Marrink SJ. Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Scientific Reports. 3: 2071. PMID 23797782 DOI: 10.1038/srep02071  1
2013 van Hell AJ, Melo MN, van Blitterswijk WJ, Gueth DM, Braumuller TM, Pedrosa LR, Song JY, Marrink SJ, Koning GA, Jonkers J, Verheij M. Defined lipid analogues induce transient channels to facilitate drug-membrane traversal and circumvent cancer therapy resistance. Scientific Reports. 3: 1949. PMID 23739489 DOI: 10.1038/Srep01949  1
2013 Marrink SJ, Tieleman DP. Perspective on the Martini model. Chemical Society Reviews. 42: 6801-22. PMID 23708257 DOI: 10.1039/c3cs60093a  1
2013 Moiset G, Cirac AD, Stuart MC, Marrink SJ, Sengupta D, Poolman B. Dual action of BPC194: a membrane active peptide killing bacterial cells. Plos One. 8: e61541. PMID 23620763 DOI: 10.1371/Journal.Pone.0061541  1
2013 Gomulya W, Costanzo GD, de Carvalho EJ, Bisri SZ, Derenskyi V, Fritsch M, Fröhlich N, Allard S, Gordiichuk P, Herrmann A, Marrink SJ, dos Santos MC, Scherf U, Loi MA. Semiconducting single-walled carbon nanotubes on demand by polymer wrapping. Advanced Materials (Deerfield Beach, Fla.). 25: 2948-56. PMID 23616236 DOI: 10.1002/Adma.201300267  1
2013 Periole X, Marrink SJ. The Martini coarse-grained force field. Methods in Molecular Biology (Clifton, N.J.). 924: 533-65. PMID 23034762 DOI: 10.1007/978-1-62703-017-5_20  1
2013 Risselada HJ, Marelli G, Fuhrmans M, Smirnova YG, Grubmüller H, Marrink SJ, Müller M. Correction: Line-Tension Controlled Mechanism for Influenza Fusion. Plos One. 8. DOI: 10.1371/Annotation/14Cda8C1-A852-4F1F-B00C-Bc45E48C8305  1
2013 Hell AJv, Melo M, Blitterswijk Wv, Dijkema T, Pedrosa L, Koning G, Marrink SJ, Jonkers J, Verheij M. Abstract 3382: Formation of transient membrane channels targets doxorubicin resistance. Cancer Research. 73: 3382-3382. DOI: 10.1158/1538-7445.Am2013-3382  1
2013 Smirnova YG, Aeffner S, Risselada HJ, Salditt T, Marrink SJ, Müller M, Knecht V. Interbilayer repulsion forces between tension-free lipid bilayers from simulation. Soft Matter. 9: 10705-10718. DOI: 10.1039/C3Sm51771C  1
2013 Liang C, Louhivuori M, Marrink SJ, Jansen TLC, Knoester J. Vibrational spectra of a mechanosensitive channel Journal of Physical Chemistry Letters. 4: 448-452. DOI: 10.1021/jz3019258  1
2013 Gobbo C, Beurroies I, De Ridder D, Eelkema R, Marrink SJ, De Feyter S, Van Esch JH, De Vries AH. MARTINI model for physisorption of organic molecules on graphite Journal of Physical Chemistry C. 117: 15623-15631. DOI: 10.1021/Jp402615P  1
2013 Uusitalo JJ, Ingólfsson HI, Marrink S. Covering All the Bases: A Martini Coarse-Grained Force Field for DNA Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.952  1
2013 Wassenaar TA, Moussatova A, Marrink S, Tieleman P. The Daft Approach for in Silico Prediction of Transmembrane Peptide Complexes Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.3667  1
2012 López CA, de Vries AH, Marrink SJ. Amylose folding under the influence of lipids. Carbohydrate Research. 364: 1-7. PMID 23128420 DOI: 10.1016/j.carres.2012.10.007  1
2012 Deplazes E, Louhivuori M, Jayatilaka D, Marrink SJ, Corry B. Structural investigation of MscL gating using experimental data and coarse grained MD simulations. Plos Computational Biology. 8: e1002683. PMID 23028281 DOI: 10.1371/Journal.Pcbi.1002683  1
2012 Vandersteen A, Masman MF, De Baets G, Jonckheere W, van der Werf K, Marrink SJ, Rozenski J, Benilova I, De Strooper B, Subramaniam V, Schymkowitz J, Rousseau F, Broersen K. Molecular plasticity regulates oligomerization and cytotoxicity of the multipeptide-length amyloid-β peptide pool. The Journal of Biological Chemistry. 287: 36732-43. PMID 22992745 DOI: 10.1074/jbc.M112.394635  1
2012 Baoukina S, Marrink SJ, Tieleman DP. Molecular structure of membrane tethers. Biophysical Journal. 102: 1866-71. PMID 22768942 DOI: 10.1016/j.bpj.2012.03.048  1
2012 Risselada HJ, Marelli G, Fuhrmans M, Smirnova YG, Grubmüller H, Marrink SJ, Müller M. Line-tension controlled mechanism for influenza fusion. Plos One. 7: e38302. PMID 22761674 DOI: 10.1371/Journal.Pone.0038302  1
2012 Periole X, Knepp AM, Sakmar TP, Marrink SJ, Huber T. Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers Journal of the American Chemical Society. 134: 10959-10965. PMID 22679925 DOI: 10.1021/Ja303286E  1
2012 Knepp AM, Periole X, Marrink SJ, Sakmar TP, Huber T. Rhodopsin forms a dimer with cytoplasmic helix 8 contacts in native membranes Biochemistry. 51: 1819-1821. PMID 22352709 DOI: 10.1021/Bi3001598  1
2012 Hell AJv, Gueth DM, Melo MN, Marrink SJ, Verheij M. Abstract 2750: Short-chain lipids catalyse intracellular drug accumulation by a transient molecular gateway that allows plasma membrane traversal Cancer Research. 72: 2750-2750. DOI: 10.1158/1538-7445.Am2012-2750  1
2012 Goga N, Rzepiela AJ, De Vries AH, Marrink SJ, Berendsen HJC. Efficient algorithms for langevin and DPD dynamics Journal of Chemical Theory and Computation. 8: 3637-3649. DOI: 10.1021/ct3000876  1
2012 Deplazes E, Jayatilaka D, Louhivuori M, Marrink S, Corry B. A Model of the Open Pore MscL Based on Experimental Data and Restrained Coarse Grained Simulations Biophysical Journal. 102: 1-1. DOI: 10.1016/J.Bpj.2011.11.680  1
2012 Moiset G, Cirac AD, Mika JT, Koçer A, Stuart MC, Sengupta D, Marrink S, Poolman B. “Multi-Hit” Action of Membrane Active Peptides: Towards Understanding Bacterial Cell Killing Biophysical Journal. 102: 616a. DOI: 10.1016/J.Bpj.2011.11.3357  0.01
2012 Huber T, Periole X, Knepp AM, Marrink S, Mukhopadhyay P, Sakmar TP. Dynamic Assembly of the Receptor-G-Protein Signaling Complex Biophysical Journal. 102: 516a. DOI: 10.1016/J.Bpj.2011.11.2823  0.01
2012 Periole X, Knepp AM, Sakmar TP, Marrink S, Huber T. Probing the Receptor Dimer Interfaces of G-Protein Coupled Receptor in Model Membranes Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.2822  1
2012 Wassenaar TA, Schafer LV, Ingolfsson H, Marrink S. Mixing Martinis: Atomistic Simulations of MscL in a Coarse Grained Environment Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.1326  1
2011 Velinova M, Sengupta D, Tadjer AV, Marrink SJ. Sphere-to-rod transitions of nonionic surfactant micelles in aqueous solution modeled by molecular dynamics simulations. Langmuir : the Acs Journal of Surfaces and Colloids. 27: 14071-7. PMID 21981373 DOI: 10.1021/La203055T  1
2011 Mika JT, Moiset G, Cirac AD, Feliu L, Bardají E, Planas M, Sengupta D, Marrink SJ, Poolman B. Structural basis for the enhanced activity of cyclic antimicrobial peptides: the case of BPC194. Biochimica Et Biophysica Acta. 1808: 2197-205. PMID 21586269 DOI: 10.1016/J.Bbamem.2011.05.001  1
2011 Cirac AD, Moiset G, Mika JT, Koçer A, Salvador P, Poolman B, Marrink SJ, Sengupta D. The molecular basis for antimicrobial activity of pore-forming cyclic peptides. Biophysical Journal. 100: 2422-31. PMID 21575576 DOI: 10.1016/J.Bpj.2011.03.057  1
2011 Risselada HJ, Marrink SJ, Müller M. Curvature-dependent elastic properties of liquid-ordered domains result in inverted domain sorting on uniaxially compressed vesicles. Physical Review Letters. 106: 148102. PMID 21561224 DOI: 10.1103/PhysRevLett.106.148102  1
2011 Rzepiela AJ, Louhivuori M, Peter C, Marrink SJ. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Physical Chemistry Chemical Physics : Pccp. 13: 10437-48. PMID 21494747 DOI: 10.1039/C0Cp02981E  1
2011 De Jong DH, Schäfer LV, De Vries AH, Marrink SJ, Berendsen HJ, Grubmüller H. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations. Journal of Computational Chemistry. 32: 1919-28. PMID 21469160 DOI: 10.1002/Jcc.21776  1
2011 López CA, de Vries AH, Marrink SJ. Molecular mechanism of cyclodextrin mediated cholesterol extraction. Plos Computational Biology. 7: e1002020. PMID 21455285 DOI: 10.1371/journal.pcbi.1002020  1
2011 Schäfer LV, de Jong DH, Holt A, Rzepiela AJ, de Vries AH, Poolman B, Killian JA, Marrink SJ. 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: 1343-8. PMID 21205902 DOI: 10.1073/Pnas.1009362108  1
2011 Fuhrmans M, Marrink SJ. A tool for the morphological analysis of mixtures of lipids and water in computer simulations. Journal of Molecular Modeling. 17: 1755-66. PMID 21061034 DOI: 10.1007/S00894-010-0858-6  1
2011 Sørensen J, Periole X, Skeby KK, Marrink S, Schiøtt B. Protofibrillar Assembly Toward the Formation of Amyloid Fibrils Journal of Physical Chemistry Letters. 2: 2385-2390. DOI: 10.1021/Jz2010094  1
2011 Periole X, Marrink S, Tieleman P. A Structurally Flexible Protein Backbone for the MARTINI Coarse Grained Force Field Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.3533  1
2011 Wassenaar TA, Louhivuori MJ, Rzepiela AJ, Marrink S. Mixing Martinis: Hybrid Atomistic/Coarse-Grained Models for Protein Molecular Dynamics Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.1891  1
2011 Deplazes E, Louhivuori M, Marrink SJ, Corry B. Modeling of the Open-Channel Structure of Mscl Using Restrained Simulations Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.1729  1
2011 Westerbeek A, Szymański W, Wijma HJ, Marrink SJ, Feringa BL, Janssen DB. Kinetic resolution of α-bromoamides: Experimental and theoretical investigation of highly enantioselective reactions catalyzed by haloalkane dehalogenases Advanced Synthesis and Catalysis. 353: 931-944. DOI: 10.1002/adsc.201000726  1
2010 Vuorela T, Catte A, Niemelä PS, Hall A, Hyvönen MT, Marrink SJ, Karttunen M, Vattulainen I. Role of lipids in spheroidal high density lipoproteins. Plos Computational Biology. 6: e1000964. PMID 21060857 DOI: 10.1371/Journal.Pcbi.1000964  1
2010 Ramadurai S, Holt A, Schäfer LV, Krasnikov VV, Rijkers DT, Marrink SJ, Killian JA, Poolman B. Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides. Biophysical Journal. 99: 1447-54. PMID 20816056 DOI: 10.1016/J.Bpj.2010.05.042  1
2010 Kucerka N, Marquardt D, Harroun TA, Nieh MP, Wassall SR, de Jong DH, Schäfer LV, Marrink SJ, Katsaras J. Cholesterol in bilayers with PUFA chains: doping with DMPC or POPC results in sterol reorientation and membrane-domain formation. Biochemistry. 49: 7485-93. PMID 20669961 DOI: 10.1021/Bi100891Z  1
2010 Lycklama A Nijeholt JA, Bulacu M, Marrink SJ, Driessen AJ. Immobilization of the plug domain inside the SecY channel allows unrestricted protein translocation. The Journal of Biological Chemistry. 285: 23747-54. PMID 20489195 DOI: 10.1074/Jbc.M110.124636  1
2010 Smirnova YG, Marrink SJ, Lipowsky R, Knecht V. Solvent-exposed tails as prestalk transition states for membrane fusion at low hydration. Journal of the American Chemical Society. 132: 6710-8. PMID 20411937 DOI: 10.1021/Ja910050X  1
2010 Marrink SJ, Periole X, Tieleman DP, de Vries AH. 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 : Pccp. 12: 2254-6; author reply. PMID 20165775 DOI: 10.1039/b915293h  1
2010 Apajalahti T, Niemelä P, Govindan PN, Miettinen MS, Salonen E, Marrink SJ, Vattulainen I. Concerted diffusion of lipids in raft-like membranes. Faraday Discussions. 144: 411-30; discussion 4. PMID 20158041 DOI: 10.1039/B901487J  1
2010 Baoukina S, Marrink SJ, Tieleman DP. Lateral pressure profiles in lipid monolayers. Faraday Discussions. 144: 393-409; discussion . PMID 20158040 DOI: 10.1039/B905647E  1
2010 Rzepiela AJ, Schäfer LV, Goga N, Risselada HJ, De Vries AH, Marrink SJ. Reconstruction of atomistic details from coarse-grained structures. Journal of Computational Chemistry. 31: 1333-43. PMID 20087907 DOI: 10.1002/jcc.21415  1
2010 Polyansky AA, Ramaswamy R, Volynsky PE, Sbalzarini IF, Marrink SJ, Efremov RG. Antimicrobial peptides induce growth of phosphatidylglycerol domains in a model bacterial membrane Journal of Physical Chemistry Letters. 1: 3108-3111. DOI: 10.1021/jz101163e  1
2010 Periole X, Huber T, Sakmar TP, Marrink S. Amyloid-Like Cross-Beta Structure Polymorphism: An Energetic Point of View Biophysical Journal. 98: 424a. DOI: 10.1016/J.Bpj.2009.12.2294  0.01
2010 Ollila SOH, Louhivuori M, Marrink S, Vattulainen I. Lateral Pressure Profile and Curvature Frustration in Mechanosensitive Channel Gating Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.121  1
2010 Fuhrmans M, Sanders BP, Marrink S, Vries AHd. Effects of bundling on the properties of the SPC water model Theoretical Chemistry Accounts. 125: 335-344. DOI: 10.1007/S00214-009-0590-4  1
2009 Periole X, Cavalli M, Marrink SJ, Ceruso MA. Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. Journal of Chemical Theory and Computation. 5: 2531-43. PMID 26616630 DOI: 10.1021/Ct9002114  1
2009 López CA, Rzepiela AJ, de Vries AH, Dijkhuizen L, Hünenberger PH, Marrink SJ. Martini Coarse-Grained Force Field: Extension to Carbohydrates. Journal of Chemical Theory and Computation. 5: 3195-210. PMID 26602504 DOI: 10.1021/ct900313w  1
2009 Hinner MJ, Marrink SJ, de Vries AH. Location, tilt, and binding: a molecular dynamics study of voltage-sensitive dyes in biomembranes. The Journal of Physical Chemistry. B. 113: 15807-19. PMID 19894688 DOI: 10.1021/jp907981y  1
2009 Sengupta D, Rampioni A, Marrink SJ. Simulations of the c-subunit of ATP-synthase reveal helix rearrangements. Molecular Membrane Biology. 26: 422-34. PMID 19878046 DOI: 10.3109/09687680903321073  1
2009 Kucerka N, Gallová J, Uhríková D, Balgavý P, Bulacu M, Marrink SJ, Katsaras J. Areas of monounsaturated diacylphosphatidylcholines. Biophysical Journal. 97: 1926-32. PMID 19804723 DOI: 10.1016/J.Bpj.2009.06.050  1
2009 Lee H, de Vries AH, Marrink SJ, Pastor RW. A coarse-grained model for polyethylene oxide and polyethylene glycol: conformation and hydrodynamics. The Journal of Physical Chemistry. B. 113: 13186-94. PMID 19754083 DOI: 10.1021/Jp9058966  1
2009 Bennett WF, MacCallum JL, Hinner MJ, Marrink SJ, Tieleman DP. Molecular view of cholesterol flip-flop and chemical potential in different membrane environments. Journal of the American Chemical Society. 131: 12714-20. PMID 19673519 DOI: 10.1021/ja903529f  1
2009 Masman MF, Eisel UL, Csizmadia IG, Penke B, Enriz RD, Marrink SJ, Luiten PG. In silico study of full-length amyloid beta 1-42 tri- and penta-oligomers in solution. The Journal of Physical Chemistry. B. 113: 11710-9. PMID 19645414 DOI: 10.1021/Jp901057W  1
2009 Yesylevskyy S, Marrink SJ, Mark AE. Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers Biophysical Journal. 97: 40-49. PMID 19580742 DOI: 10.1016/J.Bpj.2009.03.059  1
2009 Siwko ME, de Vries AH, Mark AE, Kozubek A, Marrink SJ. Disturb or stabilize? A molecular dynamics study of the effects of resorcinolic lipids on phospholipid bilayers. Biophysical Journal. 96: 3140-53. PMID 19383459 DOI: 10.1016/j.bpj.2009.01.040  1
2009 Berntsson RP, Doeven MK, Fusetti F, Duurkens RH, Sengupta D, Marrink SJ, Thunnissen AM, Poolman B, Slotboom DJ. The structural basis for peptide selection by the transport receptor OppA. The Embo Journal. 28: 1332-40. PMID 19300437 DOI: 10.1038/Emboj.2009.65  1
2009 Ollila OH, Risselada HJ, Louhivuori M, Lindahl E, Vattulainen I, Marrink SJ. 3D pressure field in lipid membranes and membrane-protein complexes. Physical Review Letters. 102: 078101. PMID 19257715 DOI: 10.1103/Physrevlett.102.078101  1
2009 Marrink SJ, de Vries AH, Tieleman DP. Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochimica Et Biophysica Acta. 1788: 149-68. PMID 19013128 DOI: 10.1016/j.bbamem.2008.10.006  1
2009 Periole X, Huber T, Marrink S, Sakmar TP. Membrane Proteins-bilayer Interplay: Insights From Coarse-grained Self-assembly And Potential Of Mean Force Simulations Of Rhodopsin In Model Bilayers Biophysical Journal. 96: 673a. DOI: 10.1016/J.Bpj.2008.12.3556  0.01
2009 Louhivuori M, Risselada J, Giessen Evd, Marrink S. MscL Gating In Liposomes Biophysical Journal. 96: 2-4. DOI: 10.1016/J.Bpj.2008.12.1254  1
2008 Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink SJ. The MARTINI Coarse-Grained Force Field: Extension to Proteins. Journal of Chemical Theory and Computation. 4: 819-34. PMID 26621095 DOI: 10.1021/Ct700324X  1
2008 Baoukina S, Monticelli L, Risselada HJ, Marrink SJ, Tieleman DP. The molecular mechanism of lipid monolayer collapse. Proceedings of the National Academy of Sciences of the United States of America. 105: 10803-8. PMID 18669655 DOI: 10.1073/pnas.0711563105  1
2008 Sengupta D, Leontiadou H, Mark AE, Marrink SJ. Toroidal pores formed by antimicrobial peptides show significant disorder Biochimica Et Biophysica Acta - Biomembranes. 1778: 2308-2317. PMID 18602889 DOI: 10.1016/J.Bbamem.2008.06.007  1
2008 Risselada HJ, Mark AE, Marrink SJ. Application of mean field boundary potentials in simulations of lipid vesicles Journal of Physical Chemistry B. 112: 7438-7447. PMID 18512884 DOI: 10.1021/jp0758519  1
2008 Treptow W, Marrink SJ, Tarek M. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. The Journal of Physical Chemistry. B. 112: 3277-82. PMID 18293960 DOI: 10.1021/Jp709675E  0.01
2008 Marrink SJ, de Vries AH, Harroun TA, Katsaras J, Wassall SR. Cholesterol shows preference for the interior of polyunsaturated lipid membranes. Journal of the American Chemical Society. 130: 10-1. PMID 18076174 DOI: 10.1021/Ja076641C  1
2008 Catte A, Patterson JC, Bashtovyy D, Jones MK, Gu F, Li L, Rampioni A, Sengupta D, Vuorela T, Niemelä P, Karttunen M, Marrink SJ, Vattulainen I, Segrest JP. Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations. Biophysical Journal. 94: 2306-19. PMID 18065479 DOI: 10.1529/biophysj.107.115857  1
2008 Knecht V, Risselada HJ, Mark AE, Marrink SJ. Electrophoretic mobility does not always reflect the charge on an oil droplet Journal of Colloid and Interface Science. 318: 477-486. PMID 18061200 DOI: 10.1016/j.jcis.2007.10.035  1
2008 Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink SJ. The MARTINI coarse-grained force field: Extension to proteins Journal of Chemical Theory and Computation. 4: 819-834. DOI: 10.1021/ct700324x  1
2007 Baoukina S, Monticelli L, Marrink SJ, Tieleman DP. Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir : the Acs Journal of Surfaces and Colloids. 23: 12617-23. PMID 17973510 DOI: 10.1021/la702286h  1
2007 Periole X, Huber T, Marrink SJ, Sakmar TP. G protein-coupled receptors self-assemble in dynamics simulations of model bilayers Journal of the American Chemical Society. 129: 10126-10132. PMID 17658882 DOI: 10.1021/Ja0706246  1
2007 Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH. The MARTINI force field: coarse grained model for biomolecular simulations. The Journal of Physical Chemistry. B. 111: 7812-24. PMID 17569554 DOI: 10.1021/jp071097f  1
2007 Leontiadou H, Mark AE, Marrink SJ. Ion transport across transmembrane pores Biophysical Journal. 92: 4209-4215. PMID 17384063 DOI: 10.1529/Biophysj.106.101295  1
2007 Knecht V, Marrink SJ. Molecular dynamics simulations of lipid vesicle fusion in atomic detail. Biophysical Journal. 92: 4254-61. PMID 17384060 DOI: 10.1529/Biophysj.106.103572  1
2007 Baron R, Trzesniak D, de Vries AH, Elsener A, Marrink SJ, van Gunsteren WF. Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 8: 452-61. PMID 17290360 DOI: 10.1002/cphc.200600658  1
2007 Siwko ME, Marrink SJ, de Vries AH, Kozubek A, Schoot Uiterkamp AJM, Mark AE. Does isoprene protect plant membranes from thermal shock? A molecular dynamics study Biochimica Et Biophysica Acta - Biomembranes. 1768: 198-206. PMID 17125733 DOI: 10.1016/j.bbamem.2006.09.023  1
2006 Tieleman DP, Marrink SJ. Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop. Journal of the American Chemical Society. 128: 12462-7. PMID 16984196 DOI: 10.1021/Ja0624321  1
2006 Leontiadou H, Mark AE, Marrink SJ. Antimicrobial peptides in action Journal of the American Chemical Society. 128: 12156-12161. PMID 16967965 DOI: 10.1021/ja062927q  1
2006 Knecht V, Mark AE, Marrink SJ. Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail Journal of the American Chemical Society. 128: 2030-2034. PMID 16464104 DOI: 10.1021/Ja056619O  1
2005 Marrink SJ, Risselada J, Mark AE. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model Chemistry and Physics of Lipids. 135: 223-244. PMID 15921980 DOI: 10.1016/j.chemphyslip.2005.03.001  1
2005 De Vries AH, Yefimov S, Mark AE, Marrink SJ. Molecular structure of the lecithin ripple phase Proceedings of the National Academy of Sciences of the United States of America. 102: 5392-5396. PMID 15809443 DOI: 10.1073/pnas.0408249102  1
2005 Knecht V, Müller M, Bonn M, Marrink SJ, Mark AE. Simulation studies of pore and domain formation in a phospholipid monolayer. The Journal of Chemical Physics. 122: 024704. PMID 15638611 DOI: 10.1063/1.1825992  1
2004 Marrink SJ, Mark AE. Molecular view of hexagonal phase formation in phospholipid membranes Biophysical Journal. 87: 3894-3900. PMID 15377528 DOI: 10.1529/Biophysj.104.048710  1
2004 Faller R, Marrink SJ. Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir : the Acs Journal of Surfaces and Colloids. 20: 7686-93. PMID 15323520 DOI: 10.1021/La0492759  0.01
2004 De Vries AH, Mark AE, Marrink SJ. Molecular Dynamics Simulation of the Spontaneous Formation of a Small DPPC Vesicle in Water in Atomistic Detail Journal of the American Chemical Society. 126: 4488-4489. PMID 15070345 DOI: 10.1021/ja0398417  1
2004 Leontiadou H, Mark AE, Marrink SJ. Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers Biophysical Journal. 86: 2156-2164. PMID 15041656 DOI: 10.1016/S0006-3495(04)74275-7  1
2003 Marrink SJ, Mark AE. The mechanism of vesicle fusion as revealed by molecular dynamics simulations Journal of the American Chemical Society. 125: 11144-11145. PMID 16220905 DOI: 10.1021/ja036138+  1
2003 Marrink SJ, Mark AE. Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles Journal of the American Chemical Society. 125: 15233-15242. PMID 14653758 DOI: 10.1021/ja0352092  1
2003 Tieleman DP, Leontiadou H, Mark AE, Marrink SJ. Simulation of pore formation in lipid bilayers by mechanical stress and electric fields Journal of the American Chemical Society. 125: 6382-6383. PMID 12785774 DOI: 10.1021/ja029504i  1
2003 Colombo G, Marrink SJ, Mark AE. Simulation of MscL gating in a bilayer under stress Biophysical Journal. 84: 2331-2337. PMID 12668441  1
2002 Marrink SJ, Tieleman DP. Molecular dynamics simulation of spontaneous membrane fusion during a cubic-hexagonal phase transition. Biophysical Journal. 83: 2386-92. PMID 12414675 DOI: 10.1016/S0006-3495(02)75252-1  1
2002 Marrink SJ, Mark AE. Molecular dynamics simulations of mixed micelles modeling human bile Biochemistry. 41: 5375-5382. PMID 11969397 DOI: 10.1021/bi015613i  1
2001 Marrink SJ, Lindahl E, Edholm O, Mark AE. Simulation of the spontaneous aggregation of phospholipids into bilayers [23] Journal of the American Chemical Society. 123: 8638-8639. PMID 11525689 DOI: 10.1021/Ja0159618  1
2001 Marrink S, Marčelja S. Potential of Mean Force Computations of Ions Approaching a Surface Langmuir. 17: 7929-7934. DOI: 10.1021/La015526R  0.56
2001 Marrink SJ, Mark AE. Effect of undulations on surface tension in simulated bilayers Journal of Physical Chemistry B. 105: 6122-6127. DOI: 10.1021/jp0103474  1
1998 Marrink SJ, Berger O, Tieleman P, Jähnig F. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. Biophysical Journal. 74: 931-43. PMID 9533704 DOI: 10.1016/S0006-3495(98)74016-0  1
1997 Tieleman DP, Marrink SJ, Berendsen HJ. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochimica Et Biophysica Acta. 1331: 235-70. PMID 9512654 DOI: 10.1016/S0304-4157(97)00008-7  1
1996 Marrink SJ, Jähnig F, Berendsen HJ. Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophysical Journal. 71: 632-47. PMID 8842203 DOI: 10.1016/S0006-3495(96)79264-0  1
1996 Marrink S, Sok RM, Berendsen HJC. Free volume properties of a simulated lipid membrane Journal of Chemical Physics. 104: 9090-9099. DOI: 10.1063/1.471442  1
1996 López Cascales JJ, De La Torre JG, Marrink SJ, Berendsen HJC. Molecular dynamics simulation of a charged biological membrane Journal of Chemical Physics. 104: 2713-2720. DOI: 10.1063/1.470992  1
1996 Marrink SJ, Tieleman DP, Van Buuren AR, Berendsen HJC. Membranes and water: An interesting relationship Faraday Discussions. 103: 191-201. DOI: 10.1039/Fd9960300191  1
1996 Marrink SJ, Berendsen HJC. Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular Dynamics Simulations The Journal of Physical Chemistry. 100: 16729-16738. DOI: 10.1021/Jp952956F  1
1995 Buuren ARv, Marrink S, Berendsen HJC. Characterisation of aqueous interfaces with different hydrophobicities by molecular dynamics Colloids and Surfaces a: Physicochemical and Engineering Aspects. 102: 143-157. DOI: 10.1016/0927-7757(95)03227-5  1
1994 Egberts E, Marrink SJ, Berendsen HJ. Molecular dynamics simulation of a phospholipid membrane. European Biophysics Journal : Ebj. 22: 423-36. PMID 8149924 DOI: 10.1007/Bf00180163  1
1994 Marrink S, Berendsen HJC. Simulation of Water Transport through a Lipid Membrane The Journal of Physical Chemistry. 98: 4155-4168. DOI: 10.1021/J100066A040  1
1993 Berendsen HJC, Marrink S. Molecular dynamics of water transport through membranes: Water from solvent to solute Pure and Applied Chemistry. 65: 2513-2520. DOI: 10.1351/Pac199365122513  1
1993 Buuren ARv, Marrink SJ, Berendsen HJC. A Molecular Dynamics Study of the Decane/Water Interface The Journal of Physical Chemistry. 97: 9206-9212. DOI: 10.1021/J100138A023  1
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