| Year |
Citation |
Score |
| 2024 |
Park P, Matsubara DK, Barzotto DR, Lima FS, Chaimovich H, Marrink SJ, Cuccovia IM. Vesicle protrusion induced by antimicrobial peptides suggests common carpet mechanism for short antimicrobial peptides. Scientific Reports. 14: 9701. PMID 38678109 DOI: 10.1038/s41598-024-60601-w |
0.307 |
|
| 2023 |
van Tilburg MPA, Marrink SJ, König M, Grünewald F. Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks. Journal of Chemical Theory and Computation. 20: 212-223. PMID 38109481 DOI: 10.1021/acs.jctc.3c00961 |
0.417 |
|
| 2023 |
Stępień P, Świątek S, Robles MYY, Markiewicz-Mizera J, Balakrishnan D, Inaba-Inoue S, De Vries AH, Beis K, Marrink SJ, Heddle JG. CRAFTing Delivery of Membrane Proteins into Protocells using Nanodiscs. Acs Applied Materials & Interfaces. 15: 56689-701. PMID 38015973 DOI: 10.1021/acsami.3c11894 |
0.318 |
|
| 2023 |
Ingólfsson HI, Rizuan A, Liu X, Mohanty P, Souza PCT, Marrink SJ, Bowers MT, Mittal J, Berry J. Multiscale simulations reveal TDP-43 molecular level interactions driving condensation. Biophysical Journal. PMID 37853696 DOI: 10.1016/j.bpj.2023.10.016 |
0.317 |
|
| 2023 |
Blanco-González A, Marrink SJ, Piñeiro Á, García-Fandiño R. Molecular insights into the effects of focused ultrasound mechanotherapy on lipid bilayers: Unlocking the keys to design effective treatments. Journal of Colloid and Interface Science. 650: 1201-1210. PMID 37478737 DOI: 10.1016/j.jcis.2023.07.077 |
0.365 |
|
| 2023 |
Melcrová A, Maity S, Melcr J, de Kok NAW, Gabler M, van der Eyden J, Stensen W, Svendsen JSM, Driessen AJM, Marrink SJ, Roos WH. Lateral membrane organization as target of an antimicrobial peptidomimetic compound. Nature Communications. 14: 4038. PMID 37419980 DOI: 10.1038/s41467-023-39726-5 |
0.311 |
|
| 2023 |
Empereur-Mot C, Pedersen KB, Capelli R, Crippa M, Caruso C, Perrone M, Souza PCT, Marrink SJ, Pavan GM. Automatic Optimization of Lipid Models in the Martini Force Field Using . Journal of Chemical Information and Modeling. 63: 3827-3838. PMID 37279107 DOI: 10.1021/acs.jcim.3c00530 |
0.37 |
|
| 2023 |
Pezeshkian W, Grünewald F, Narykov O, Lu S, Arkhipova V, Solodovnikov A, Wassenaar TA, Marrink SJ, Korkin D. Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling. Structure (London, England : 1993). PMID 36870335 DOI: 10.1016/j.str.2023.02.006 |
0.347 |
|
| 2023 |
Hilpert C, Beranger L, Souza PCT, Vainikka PA, Nieto V, Marrink SJ, Monticelli L, Launay G. Facilitating CG Simulations with MAD: The MArtini Database Server. Journal of Chemical Information and Modeling. PMID 36656159 DOI: 10.1021/acs.jcim.2c01375 |
0.354 |
|
| 2022 |
De Franceschi N, Pezeshkian W, Fragasso A, Bruininks BMH, Tsai S, Marrink SJ, Dekker C. Synthetic Membrane Shaper for Controlled Liposome Deformation. Acs Nano. PMID 36441529 DOI: 10.1021/acsnano.2c06125 |
0.332 |
|
| 2022 |
Grünewald F, Punt MH, Jefferys EE, Vainikka PA, König M, Virtanen V, Meyer TA, Pezeshkian W, Gormley AJ, Karonen M, Sansom MSP, Souza PCT, Marrink SJ. Martini 3 Coarse-Grained Force Field for Carbohydrates. Journal of Chemical Theory and Computation. PMID 36342474 DOI: 10.1021/acs.jctc.2c00757 |
0.349 |
|
| 2022 |
Frallicciardi J, Melcr J, Siginou P, Marrink SJ, Poolman B. Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes. Nature Communications. 13: 1605. PMID 35338137 DOI: 10.1038/s41467-022-29272-x |
0.343 |
|
| 2021 |
Azadi-Chegeni F, Thallmair S, Ward ME, Perin G, Marrink SJ, Baldus M, Morosinotto T, Pandit A. Protein dynamics and lipid affinity of monomeric, zeaxanthin-binding LHCII in thylakoid membranes. Biophysical Journal. PMID 34971616 DOI: 10.1016/j.bpj.2021.12.039 |
0.358 |
|
| 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 |
0.312 |
|
| 2021 |
Bruininks BMH, Thie AS, Souza PCT, Wassenaar TA, Faraji S, Marrink SJ. Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies. Journal of Chemical Theory and Computation. PMID 34609876 DOI: 10.1021/acs.jctc.1c00446 |
0.669 |
|
| 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 |
0.393 |
|
| 2021 |
Tsanai M, Frederix PWJM, Schroer CFE, Souza PCT, Marrink SJ. Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model. Chemical Science. 12: 8521-8530. PMID 34221333 DOI: 10.1039/d1sc00374g |
0.317 |
|
| 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 |
0.341 |
|
| 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 |
0.376 |
|
| 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 |
0.318 |
|
| 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 |
0.328 |
|
| 2021 |
Pezeshkian W, Marrink SJ. Simulating realistic membrane shapes. Current Opinion in Cell Biology. 71: 103-111. PMID 33721706 DOI: 10.1016/j.ceb.2021.02.009 |
0.349 |
|
| 2021 |
Grünewald F, Kroon PC, Souza PCT, Marrink SJ. Protocol for Simulations of PEGylated Proteins with Martini 3. Methods in Molecular Biology (Clifton, N.J.). 2199: 315-335. PMID 33125658 DOI: 10.1007/978-1-0716-0892-0_18 |
0.31 |
|
| 2020 |
Grünewald F, Souza PCT, Abdizadeh H, Barnoud J, de Vries AH, Marrink SJ. Titratable Martini model for constant pH simulations. The Journal of Chemical Physics. 153: 024118. PMID 32668918 DOI: 10.1063/5.0014258 |
0.311 |
|
| 2020 |
Pezeshkian W, König M, Wassenaar TA, Marrink SJ. Backmapping triangulated surfaces to coarse-grained membrane models. Nature Communications. 11: 2296. PMID 32385270 DOI: 10.1038/s41467-020-16094-y |
0.396 |
|
| 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 |
0.392 |
|
| 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 |
0.338 |
|
| 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 |
0.314 |
|
| 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 |
0.37 |
|
| 2020 |
Bruininks BMH, Souza PCT, Marrink SJ. A Practical View of the Martini Force Field. Methods in Molecular Biology (Clifton, N.J.). 2022: 105-127. PMID 31396901 DOI: 10.1007/978-1-4939-9608-7_5 |
0.301 |
|
| 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 |
0.36 |
|
| 2019 |
Pezeshkian W, König M, Marrink SJ, Ipsen JH. A Multi-Scale Approach to Membrane Remodeling Processes. Frontiers in Molecular Biosciences. 6: 59. PMID 31396522 DOI: 10.3389/fmolb.2019.00059 |
0.336 |
|
| 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 |
0.359 |
|
| 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 |
0.597 |
|
| 2019 |
Thallmair S, Vainikka PA, Marrink SJ. Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes. Biophysical Journal. 116: 1446-1455. PMID 30954210 DOI: 10.1016/j.bpj.2019.03.009 |
0.374 |
|
| 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 |
0.352 |
|
| 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 |
0.364 |
|
| 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 |
0.383 |
|
| 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 |
0.316 |
|
| 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 |
0.323 |
|
| 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 |
0.427 |
|
| 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 |
0.376 |
|
| 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 |
0.336 |
|
| 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 |
0.364 |
|
| 2018 |
Zavadlav J, Marrink SJ, Praprotnik M. Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm. Journal of Chemical Theory and Computation. 14: 1754-1761. PMID 29439560 DOI: 10.1021/acs.jctc.7b01129 |
0.301 |
|
| 2018 |
Van Eerden FJ, Melo MN, Frederix PWJM, Marrink SJ. Prediction of Thylakoid Lipid Binding Sites on Photosystem II. Biophysical Journal. 113: 2669-2681. PMID 29262360 DOI: 10.1016/j.bpj.2017.09.039 |
0.347 |
|
| 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 |
0.34 |
|
| 2018 |
Baoukina S, Ingolfsson HI, Marrink SJ, Tieleman DP. Lipid Organization in Simulations of Cell Membranes Biophysical Journal. 114: 379a. DOI: 10.1016/j.bpj.2017.11.2099 |
0.315 |
|
| 2017 |
Kondela T, Gallová J, Hauß T, Barnoud J, Marrink SJ, Kučerka N. Alcohol Interactions with Lipid Bilayers. Molecules (Basel, Switzerland). 22. PMID 29182554 DOI: 10.3390/molecules22122078 |
0.343 |
|
| 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 |
0.312 |
|
| 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 |
0.4 |
|
| 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 |
0.373 |
|
| 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 |
0.623 |
|
| 2016 |
Arnarez C, Marrink SJ, Periole X. Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes. Chemical Science. 7: 4435-4443. PMID 30155091 DOI: 10.1039/c5sc04664e |
0.342 |
|
| 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 |
0.306 |
|
| 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 |
0.383 |
|
| 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 |
0.388 |
|
| 2016 |
Ingólfsson HI, Arnarez C, Periole X, Marrink SJ. Computational 'microscopy' of cellular membranes. Journal of Cell Science. 129: 257-68. PMID 26743083 DOI: 10.1242/jcs.176040 |
0.34 |
|
| 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 |
0.381 |
|
| 2016 |
Gu R, Ingolfsson HI, de Vries AH, Marrink SJ, Tieleman DP. Ganglioside and Protein-Ganglioside Interactions in Martini and Atomistic Molecular Dynamics Simulations Biophysical Journal. 110: 254a. DOI: 10.1016/J.BPJ.2015.11.1395 |
0.308 |
|
| 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 |
0.313 |
|
| 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 |
0.355 |
|
| 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 |
0.411 |
|
| 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 |
0.368 |
|
| 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 |
0.412 |
|
| 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 |
0.302 |
|
| 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 |
0.355 |
|
| 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 |
0.337 |
|
| 2015 |
Wassenaar TA, Pluhackova K, Moussatova A, Sengupta D, Marrink SJ, Tieleman DP, Böckmann RA. Landscapes of Membrane Protein Interactions from High-Throughput MD Simulations using the Daft Approach Biophysical Journal. 108: 526a. DOI: 10.1016/J.BPJ.2014.11.2885 |
0.346 |
|
| 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 |
0.321 |
|
| 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 |
0.313 |
|
| 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 |
0.355 |
|
| 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 |
0.323 |
|
| 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 |
0.35 |
|
| 2014 |
Pannuzzo M, De Jong DH, Raudino A, Marrink SJ. Simulation of polyethylene glycol and calcium-mediated membrane fusion. The Journal of Chemical Physics. 140: 124905. PMID 24697479 DOI: 10.1063/1.4869176 |
0.351 |
|
| 2014 |
Zavadlav J, Melo MN, Marrink SJ, Praprotnik M. Adaptive resolution simulation of an atomistic protein in MARTINI water. The Journal of Chemical Physics. 140: 054114. PMID 24511929 DOI: 10.1063/1.4863329 |
0.304 |
|
| 2014 |
Raudino A, Marrink SJ, Pannuzzo M. Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: a theoretical and computational study. The Journal of Chemical Physics. 138: 234901. PMID 23802979 DOI: 10.1063/1.4809993 |
0.347 |
|
| 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 |
0.405 |
|
| 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 |
0.395 |
|
| 2014 |
Periole X, Sakmar TP, Marrink SJ, Huber T. Supramolecular Organization of Rod Outer Segment Membrane: New Rhodopsin Dimer Interface and Insights from the β2Ar-Gs Complex Biophysical Journal. 106: 305a-306a. DOI: 10.1016/J.Bpj.2013.11.1772 |
0.344 |
|
| 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 |
0.466 |
|
| 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 |
0.317 |
|
| 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 |
0.405 |
|
| 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 |
0.328 |
|
| 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 |
0.358 |
|
| 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 |
0.304 |
|
| 2013 |
Wassenaar TA, Ingólfsson HI, Priess M, Marrink SJ, Schäfer LV. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations. The Journal of Physical Chemistry. B. 117: 3516-30. PMID 23406326 DOI: 10.1021/jp311533p |
0.342 |
|
| 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 |
0.336 |
|
| 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 |
0.418 |
|
| 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 |
0.362 |
|
| 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 |
0.725 |
|
| 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 |
0.398 |
|
| 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 |
0.385 |
|
| 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 |
0.327 |
|
| 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 |
0.4 |
|
| 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 |
0.397 |
|
| 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 |
0.365 |
|
| 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 |
0.413 |
|
| 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 |
0.451 |
|
| 2011 |
Bulacu M, Périole X, Marrink SJ. In silico design of robust bolalipid membranes. Biomacromolecules. 13: 196-205. PMID 22103705 DOI: 10.1021/bm201454j |
0.356 |
|
| 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 |
0.357 |
|
| 2011 |
Domański J, Marrink SJ, Schäfer LV. Transmembrane helices can induce domain formation in crowded model membranes. Biochimica Et Biophysica Acta. 1818: 984-94. PMID 21884678 DOI: 10.1016/j.bbamem.2011.08.021 |
0.352 |
|
| 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 |
0.602 |
|
| 2011 |
Samuli Ollila OH, Louhivuori M, Marrink SJ, Vattulainen I. Protein shape change has a major effect on the gating energy of a mechanosensitive channel. Biophysical Journal. 100: 1651-9. PMID 21463578 DOI: 10.1016/j.bpj.2011.02.027 |
0.382 |
|
| 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 |
0.38 |
|
| 2011 |
Schäfer LV, Marrink SJ. Partitioning of lipids at domain boundaries in model membranes. Biophysical Journal. 99: L91-3. PMID 21156123 DOI: 10.1016/j.bpj.2010.08.072 |
0.367 |
|
| 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 |
0.379 |
|
| 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 |
0.725 |
|
| 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 |
0.415 |
|
| 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 |
0.413 |
|
| 2010 |
Sengupta D, Marrink SJ. Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes. Physical Chemistry Chemical Physics : Pccp. 12: 12987-96. PMID 20733990 DOI: 10.1039/c0cp00101e |
0.314 |
|
| 2010 |
Yesylevskyy SO, Schäfer LV, Sengupta D, Marrink SJ. Polarizable water model for the coarse-grained MARTINI force field. Plos Computational Biology. 6: e1000810. PMID 20548957 DOI: 10.1371/journal.pcbi.1000810 |
0.301 |
|
| 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 |
0.478 |
|
| 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 |
0.423 |
|
| 2010 |
Esteban-Martín S, Risselada HJ, Salgado J, Marrink SJ. Stability of asymmetric lipid bilayers assessed by molecular dynamics simulations. Journal of the American Chemical Society. 131: 15194-202. PMID 19795891 DOI: 10.1021/ja904450t |
0.418 |
|
| 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 |
0.357 |
|
| 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 |
0.428 |
|
| 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 |
0.363 |
|
| 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 |
0.416 |
|
| 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 |
0.392 |
|
| 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 |
0.36 |
|
| 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 |
0.373 |
|
| 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 |
0.362 |
|
| 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 |
0.344 |
|
| 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 |
0.41 |
|
| 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 |
0.405 |
|
| 2009 |
Risselada HJ, Marrink SJ. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations. Physical Chemistry Chemical Physics : Pccp. 11: 2056-67. PMID 19280016 DOI: 10.1039/b818782g |
0.383 |
|
| 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 |
0.311 |
|
| 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 |
0.372 |
|
| 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 |
0.496 |
|
| 2009 |
Bulacu M, Marrink SJ. Self-assembly and Equilibration of Bolalipid Membranes Studied by Molecular Dynamics Simulations Biophysical Journal. 96: 460a. DOI: 10.1016/J.BPJ.2008.12.2365 |
0.311 |
|
| 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 |
0.402 |
|
| 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 |
0.435 |
|
| 2008 |
Risselada HJ, Marrink SJ. The molecular face of lipid rafts in model membranes. Proceedings of the National Academy of Sciences of the United States of America. 105: 17367-72. PMID 18987307 DOI: 10.1073/pnas.0807527105 |
0.35 |
|
| 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 |
0.328 |
|
| 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 |
0.397 |
|
| 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 |
0.347 |
|
| 2008 |
Yefimov S, van der Giessen E, Onck PR, Marrink SJ. Mechanosensitive membrane channels in action. Biophysical Journal. 94: 2994-3002. PMID 18192351 DOI: 10.1529/biophysj.107.119966 |
0.352 |
|
| 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 |
0.482 |
|
| 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 |
0.318 |
|
| 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 |
0.379 |
|
| 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 |
0.482 |
|
| 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 |
0.513 |
|
| 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 |
0.336 |
|
| 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 |
0.449 |
|
| 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 |
0.355 |
|
| 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 |
0.38 |
|
| 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 |
0.422 |
|
| 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 |
0.327 |
|
| 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 |
0.396 |
|
| 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+ |
0.404 |
|
| 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 |
0.37 |
|
| 2003 |
Colombo G, Marrink SJ, Mark AE. Simulation of MscL gating in a bilayer under stress Biophysical Journal. 84: 2331-2337. PMID 12668441 |
0.359 |
|
| 2003 |
Anézo C, de Vries AH, Höltje H, Tieleman DP, Marrink S. Methodological Issues in Lipid Bilayer Simulations The Journal of Physical Chemistry B. 107: 9424-9433. DOI: 10.1021/JP0348981 |
0.301 |
|
| 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 |
0.4 |
|
| 2002 |
Marrink SJ, Mark AE. Molecular dynamics simulations of mixed micelles modeling human bile Biochemistry. 41: 5375-5382. PMID 11969397 DOI: 10.1021/bi015613i |
0.36 |
|
| 2002 |
Marrink SJ, Tieleman DP. Molecular dynamics simulation of a lipid diamond cubic phase. Journal of the American Chemical Society. 123: 12383-91. PMID 11734042 DOI: 10.1021/JA016012H |
0.339 |
|
| 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 |
0.409 |
|
| 2001 |
Marrink S, Marčelja S. Potential of Mean Force Computations of Ions Approaching a Surface Langmuir. 17: 7929-7934. DOI: 10.1021/La015526R |
0.308 |
|
| 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 |
0.379 |
|
| 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 |
0.635 |
|
| 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 |
0.647 |
|
| 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 |
0.363 |
|
| 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 |
0.409 |
|
| 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 |
0.379 |
|
| 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 |
0.385 |
|
| 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 |
0.689 |
|
| 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 |
0.456 |
|
| 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 |
0.453 |
|
| 1993 |
Marrink SJ, Berkowitz M, Berendsen HJC. Molecular dynamics simulation of a membrane/water interface: the ordering of water and its relation to the hydration force Langmuir. 9: 3122-3131. DOI: 10.1021/La00035A062 |
0.338 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 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/j.ceb.2014.03.006 |
0.3 |
|
| 2021 |
Liaci AM, Steigenberger B, Telles de Souza PC, Tamara S, Gröllers-Mulderij M, Ogrissek P, Marrink SJ, Scheltema RA, Förster F. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Molecular Cell. PMID 34388369 DOI: 10.1016/j.molcel.2021.07.031 |
0.3 |
|
| 2004 |
Marrink SJ, de Vries AH, Mark AE. Coarse Grained Model for Semiquantitative Lipid Simulations The Journal of Physical Chemistry B. 108: 750-760. DOI: 10.1021/JP036508G |
0.298 |
|
| 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 |
0.298 |
|
| 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 |
0.298 |
|
| 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 |
0.298 |
|
| 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 |
0.297 |
|
| 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 |
0.297 |
|
| 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 |
0.297 |
|
| 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 |
0.296 |
|
| 2013 |
Hu M, de Jong DH, Marrink SJ, Deserno M. Determining the Gaussian Curvature Modulus of Lipid Membranes in Simulations: A Comparative Study via Global Shape Transformations and Local Stress Distributions Biophysical Journal. 104: 244a. DOI: 10.1016/J.Bpj.2012.11.1373 |
0.296 |
|
| 2010 |
Sengupta D, Louhivuori M, Marrink SJ. Poration of Lipid Vesicles By Antimicrobial Peptides: Simulation Studies With a Polarizable Coarse-Grain Model Biophysical Journal. 98: 81a. DOI: 10.1016/J.BPJ.2009.12.459 |
0.296 |
|
| 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 |
0.296 |
|
| 2000 |
Marrink SJ, Tieleman DP, Mark AE. Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation The Journal of Physical Chemistry B. 104: 12165-12173. DOI: 10.1021/JP001898H |
0.296 |
|
| 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 |
0.295 |
|
| 2023 |
Sami S, Marrink SJ. Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 37327401 DOI: 10.1021/acs.jctc.2c01186 |
0.295 |
|
| 2016 |
Zavadlav J, Melo MN, Marrink SJ, Praprotnik M. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models. The Journal of Chemical Physics. 142: 244118. PMID 26133421 DOI: 10.1063/1.4923008 |
0.295 |
|
| 2010 |
Marrink SJ, Fuhrmans M, Sengupta D, Yesylevskyy S, Mark AE. Simulation Studies of Peptide Induced Membrane Poration and Fusion Biophysical Journal. 98: 435a. DOI: 10.1016/J.BPJ.2009.12.2361 |
0.294 |
|
| 2018 |
Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chemical Society Reviews. 47: 3470-3489. PMID 29688238 DOI: 10.1039/c8cs00040a |
0.292 |
|
| 2012 |
Markvoort AJ, Marrink SJ. Lipid acrobatics in the membrane fusion arena. Current Topics in Membranes. 68: 259-94. PMID 21771503 DOI: 10.1016/B978-0-12-385891-7.00011-8 |
0.292 |
|
| 2010 |
de Jong D, Periole X, Marrink SJ. Towards Molecular Dynamics Simulations of Large Protein Complexes Biophysical Journal. 98: 57a. DOI: 10.1016/J.BPJ.2009.12.329 |
0.291 |
|
| 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 |
0.29 |
|
| 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 |
0.289 |
|
| 2022 |
Grünewald F, Alessandri R, Kroon PC, Monticelli L, Souza PCT, Marrink SJ. Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials. Nature Communications. 13: 68. PMID 35013176 DOI: 10.1038/s41467-021-27627-4 |
0.289 |
|
| 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 |
0.289 |
|
| 2018 |
Thallmair S, Ingólfsson HI, Marrink SJ. Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models. The Journal of Physical Chemistry Letters. 9: 5527-5533. PMID 30192549 DOI: 10.1021/acs.jpclett.8b01877 |
0.287 |
|
| 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 |
0.286 |
|
| 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 |
0.285 |
|
| 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 |
0.285 |
|
| 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 |
0.284 |
|
| 2020 |
Faustino I, Abdizadeh H, Souza PCT, Jeucken A, Stanek WK, Guskov A, Slotboom DJ, Marrink SJ. Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nature Communications. 11: 1763. PMID 32273501 DOI: 10.1038/s41467-020-15554-9 |
0.284 |
|
| 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 |
0.284 |
|
| 2018 |
Souza PC, Wassenaar TA, Skaf MS, Marrink SJ. TLR4 Recruitment into Lipid Rafts Studied by Coarse Grained MD Simulation Biophysical Journal. 114: 72a. DOI: 10.1016/J.Bpj.2017.11.440 |
0.283 |
|
| 2017 |
Van Eerden FJ, Melo MN, Frederix PWJM, Periole X, Marrink SJ. Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. Nature Communications. 8: 15214. PMID 28489071 DOI: 10.1038/ncomms15214 |
0.283 |
|
| 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 |
0.283 |
|
| 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 |
0.283 |
|
| 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 |
0.283 |
|
| 2021 |
Nemchinova M, Melcr J, Wassenaar TA, Marrink SJ, Guskov A. Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. 61: 2407-2417. PMID 33886304 DOI: 10.1021/acs.jcim.1c00261 |
0.281 |
|
| 2014 |
Wijma HJ, Marrink SJ, Janssen DB. Computationally efficient and accurate enantioselectivity modeling by clusters of molecular dynamics simulations. Journal of Chemical Information and Modeling. 54: 2079-92. PMID 24916632 DOI: 10.1021/ci500126x |
0.279 |
|
| 2020 |
Bruininks BM, Souza PC, Ingolfsson H, Marrink SJ. A molecular view on the escape of lipoplexed DNA from the endosome. Elife. 9. PMID 32297853 DOI: 10.7554/eLife.52012 |
0.278 |
|
| 2018 |
Schroer CF, Marrink SJ. Large-Scale Coarse Grained Simulations of F-Actin Interacting with Model Membranes Biophysical Journal. 114: 648a. DOI: 10.1016/j.bpj.2017.11.3501 |
0.277 |
|
| 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 |
0.276 |
|
| 2010 |
Rzepiela AJ, Sengupta D, Goga N, Marrink SJ. Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions. Faraday Discussions. 144: 431-43; discussion 4. PMID 20158042 DOI: 10.1039/B901615E |
0.276 |
|
| 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 |
0.275 |
|
| 2009 |
Risselada HJ, Marrink SJ. The freezing process of small lipid vesicles at molecular resolution Soft Matter. 5: 4531. DOI: 10.1039/B913210D |
0.274 |
|
| 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 |
0.274 |
|
| 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 |
0.272 |
|
| 2013 |
Arnarez C, Mazat JP, Elezgaray J, Marrink SJ, Periole X. Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1. Journal of the American Chemical Society. 135: 3112-20. PMID 23363024 DOI: 10.1021/ja310577u |
0.267 |
|
| 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 |
0.266 |
|
| 2012 |
Knepp AM, Periole X, Mukhopadhyay P, Marrink SJ, Sakmar TP, Huber T. Biochemical Crosslinking and Liquid Chromatography-Mass Spectrometry Demonstrate a Rhodopsin Dimerization Interface Mediated by Helices 1 and 8 Biophysical Journal. 102: 239a. DOI: 10.1016/J.Bpj.2011.11.1315 |
0.266 |
|
| 2019 |
Thallmair S, Marrink SJ. Chromophore arrangement in light-harvesting complex II influenced by the protein dynamics on the microsecond time scale Epj Web of Conferences. 205: 09039. DOI: 10.1051/EPJCONF/201920509039 |
0.265 |
|
| 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 |
0.265 |
|
| 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 |
0.265 |
|
| 2016 |
Ingolfsson HI, Melo MN, Baoukina S, Wassenaar TA, Periole X, de Vries AH, Tieleman DP, Marrink SJ. In Silico Modeling of Biologically Complex Membranes Biophysical Journal. 110: 83a. DOI: 10.1016/J.BPJ.2015.11.505 |
0.262 |
|
| 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 |
0.261 |
|
| 2023 |
Borges-Araújo L, Borges-Araújo AC, Ozturk TN, Ramirez-Echemendia DP, Fábián B, Carpenter TS, Thallmair S, Barnoud J, Ingólfsson HI, Hummer G, Tieleman DP, Marrink SJ, Souza PCT, Melo MN. Martini 3 Coarse-Grained Force Field for Cholesterol. Journal of Chemical Theory and Computation. 19: 7387-7404. PMID 37796943 DOI: 10.1021/acs.jctc.3c00547 |
0.261 |
|
| 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 |
0.259 |
|
| 2014 |
Uusitalo J, Ingólfsson HI, Akhshi P, Tieleman DP, Poolman B, Herrmann A, Marrink SJ. Coarse-Grained Modeling of DNA-Vesicle Systems with the Martini Force Field Biophysical Journal. 106: 803a. DOI: 10.1016/J.Bpj.2013.11.4402 |
0.259 |
|
| 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 |
0.259 |
|
| 2016 |
Zavadlav J, Marrink SJ, Praprotnik M. Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles. Journal of Chemical Theory and Computation. 12: 4138-45. PMID 27409519 DOI: 10.1021/acs.jctc.6b00536 |
0.258 |
|
| 2024 |
van der Sleen L, Stevens JA, Marrink SJ, Poolman B, Tych K. Probing the stability and interdomain interactions in the ABC transporter OpuA using single-molecule optical tweezers. Cell Reports. 43: 114110. PMID 38607912 DOI: 10.1016/j.celrep.2024.114110 |
0.258 |
|
| 2012 |
Fuhrmans M, Marrink SJ. Molecular view of the role of fusion peptides in promoting positive membrane curvature. Journal of the American Chemical Society. 134: 1543-52. PMID 22191854 DOI: 10.1021/ja207290b |
0.258 |
|
| 2023 |
Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. Journal of Chemical Theory and Computation. PMID 37788237 DOI: 10.1021/acs.jctc.3c00733 |
0.256 |
|
| 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 |
0.253 |
|
| 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 |
0.251 |
|
| 2010 |
Louhivuori M, Risselada HJ, van der Giessen E, Marrink SJ. Release of content through mechano-sensitive gates in pressurized liposomes. Proceedings of the National Academy of Sciences of the United States of America. 107: 19856-60. PMID 21041677 DOI: 10.1073/pnas.1001316107 |
0.249 |
|
| 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 |
0.248 |
|
| 2017 |
Alessandri R, Uusitalo JJ, de Vries AH, Havenith RW, Marrink SJ. Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations. Journal of the American Chemical Society. 139: 3697-3705. PMID 28209056 DOI: 10.1021/jacs.6b11717 |
0.248 |
|
| 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 |
0.247 |
|
| 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 |
0.246 |
|
| 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 |
0.246 |
|
| 2018 |
Baoukina S, Ingólfsson HI, Marrink SJ, Tieleman DP. Curvature-Induced Sorting of Lipids in Plasma Membrane Tethers Advanced Theory and Simulations. 1: 1800034. DOI: 10.1002/ADTS.201800034 |
0.245 |
|
| 2016 |
Baoukina S, Ingolfsson HI, Marrink SJ, Tieleman DP. Curvature-Induced Lipid Sorting in Plasma Membrane Tethers Biophysical Journal. 110: 580a. DOI: 10.1016/J.BPJ.2015.11.3101 |
0.245 |
|
| 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 |
0.245 |
|
| 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 |
0.244 |
|
| 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 |
0.242 |
|
| 2020 |
Patmanidis I, de Vries AH, Wassenaar TA, Wang W, Portale G, Marrink SJ. Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS. Physical Chemistry Chemical Physics : Pccp. 22: 21083-21093. PMID 32945311 DOI: 10.1039/d0cp03282d |
0.241 |
|
| 2004 |
de Vries AH, Mark AE, Marrink SJ. The Binary Mixing Behavior of Phospholipids in a Bilayer: A Molecular Dynamics Study The Journal of Physical Chemistry B. 108: 2454-2463. DOI: 10.1021/JP0366926 |
0.241 |
|
| 2020 |
Souza PCT, Thallmair S, Conflitti P, Ramírez-Palacios C, Alessandri R, Raniolo S, Limongelli V, Marrink SJ. Protein-ligand binding with the coarse-grained Martini model. Nature Communications. 11: 3714. PMID 32709852 DOI: 10.1038/s41467-020-17437-5 |
0.24 |
|
| 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 |
0.24 |
|
| 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 |
0.238 |
|
| 2009 |
Fuhrmans M, Knecht V, Marrink SJ. A single bicontinuous cubic phase induced by fusion peptides. Journal of the American Chemical Society. 131: 9166-7. PMID 19530654 DOI: 10.1021/ja903224q |
0.237 |
|
| 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 |
0.237 |
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| 2022 |
Thallmair V, Schultz L, Zhao W, Marrink SJ, Oliver D, Thallmair S. Two cooperative binding sites sensitize PI(4,5)P recognition by the tubby domain. Science Advances. 8: eabp9471. PMID 36070381 DOI: 10.1126/sciadv.abp9471 |
0.236 |
|
| 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 |
0.235 |
|
| 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 |
0.232 |
|
| 2016 |
van Eijk MC, Bergsma M, Marrink SJ. Association behaviour of glucitol amine gemini surfactants : Self-consistent-field theory and molecular-dynamics simulations. The European Physical Journal. E, Soft Matter. 7: 317-24. PMID 27638163 DOI: 10.1140/epje/i2002-10012-6 |
0.232 |
|
| 2012 |
de Jong DH, Periole X, Marrink SJ. Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields. Journal of Chemical Theory and Computation. 8: 1003-14. PMID 26593362 DOI: 10.1021/ct200599d |
0.232 |
|
| 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 |
0.232 |
|
| 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 |
0.231 |
|
| 2011 |
Murtola T, Vuorela TA, Hyvönen MT, Marrink S, Karttunen M, Vattulainen I. Low density lipoprotein: structure, dynamics, and interactions of apoB-100 with lipids Soft Matter. 7: 8135. DOI: 10.1039/C1SM05367A |
0.23 |
|
| 2022 |
Patmanidis I, Souza PCT, Sami S, Havenith RWA, de Vries AH, Marrink SJ. Modelling structural properties of cyanine dye nanotubes at coarse-grained level. Nanoscale Advances. 4: 3033-3042. PMID 36133510 DOI: 10.1039/d2na00158f |
0.228 |
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| 2023 |
Tharmasothirajan A, Melcr J, Linney J, Gensch T, Krumbach K, Ernst KM, Brasnett C, Poggi P, Pitt AR, Goddard AD, Chatgilialoglu A, Marrink SJ, Marienhagen J. Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis. Nature Communications. 14: 5619. PMID 37699874 DOI: 10.1038/s41467-023-40947-x |
0.227 |
|
| 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 |
0.225 |
|
| 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 |
0.225 |
|
| 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 |
0.224 |
|
| 2013 |
Arnarez C, Marrink SJ, Periole X. Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels. Scientific Reports. 3: 1263. PMID 23405277 DOI: 10.1038/srep01263 |
0.224 |
|
| 2015 |
Ingolfsson HI, Tieleman P, Marrink S. Lipid Organization of the Plasma Membrane Biophysical Journal. 108: 358a. DOI: 10.1016/j.bpj.2014.11.1962 |
0.224 |
|
| 2018 |
Marrink SJ. Computational Modeling of Realistic Cell Membranes Biophysical Journal. 114: 367a. DOI: 10.1016/J.BPJ.2017.11.2032 |
0.224 |
|
| 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 |
0.221 |
|
| 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 |
0.22 |
|
| 2018 |
Arnarez C, Marrink SJ, Melo MN. Analyzing Simulations of Lipid Mixtures: Phase Boundaries, Tie-Lines and Critical Points Biophysical Journal. 114: 449a. DOI: 10.1016/J.BPJ.2017.11.2483 |
0.219 |
|
| 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 |
0.219 |
|
| 2023 |
Stevens JA, Grünewald F, van Tilburg PAM, König M, Gilbert BR, Brier TA, Thornburg ZR, Luthey-Schulten Z, Marrink SJ. Molecular dynamics simulation of an entire cell. Frontiers in Chemistry. 11: 1106495. PMID 36742032 DOI: 10.3389/fchem.2023.1106495 |
0.219 |
|
| 2018 |
Thallmair S, Vainikka PA, Marrink S. Molecular Dynamcis of Light-Harvesting Complex II Embedded in the Thylakoid Membrane Biophysical Journal. 114: 522a. DOI: 10.1016/J.BPJ.2017.11.2853 |
0.219 |
|
| 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 |
0.216 |
|
| 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 |
0.214 |
|
| 2011 |
Klacsová M, Bulacu M, Kučerka N, Uhríková D, Teixeira J, Marrink SJ, Balgavý P. The effect of aliphatic alcohols on fluid bilayers in unilamellar DOPC vesicles--a small-angle neutron scattering and molecular dynamics study. Biochimica Et Biophysica Acta. 1808: 2136-46. PMID 21554856 DOI: 10.1016/j.bbamem.2011.04.010 |
0.213 |
|
| 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 |
0.212 |
|
| 2010 |
Rzepiela AJ, Louhivuori M, Marrink SJ. Hybrid Simulations: Atomistic Peptides in Coarse Grained Solvent Biophysical Journal. 98: 570a. DOI: 10.1016/J.BPJ.2009.12.3092 |
0.212 |
|
| 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 |
0.212 |
|
| 2023 |
Vainikka P, Marrink SJ. Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches. Journal of Chemical Theory and Computation. 19: 596-604. PMID 36625495 DOI: 10.1021/acs.jctc.2c00796 |
0.211 |
|
| 2019 |
Zavadlav J, Marrink SJ, Praprotnik M. SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus. 9: 20180075. PMID 31065343 DOI: 10.1098/rsfs.2018.0075 |
0.21 |
|
| 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 |
0.207 |
|
| 2009 |
Bennett WD, MacCallum JL, Hinner MJ, Marrink SJ, Tieleman DP. Cholesterol Flip-flop And Chemical Potential In A Systematic Set Of Lipid Bilayers Biophysical Journal. 96: 162a. DOI: 10.1016/J.BPJ.2008.12.742 |
0.206 |
|
| 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 |
0.203 |
|
| 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 |
0.202 |
|
| 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 |
0.202 |
|
| 2019 |
Souza PCT, Thallmair S, Marrink SJ, Mera-Adasme R. An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation. The Journal of Physical Chemistry Letters. 10: 7740-7744. PMID 31747286 DOI: 10.1021/acs.jpclett.9b02868 |
0.202 |
|
| 2019 |
Alessandri R, Souza PCT, Thallmair S, Melo MN, de Vries AH, Marrink SJ. Pitfalls of the Martini Model. Journal of Chemical Theory and Computation. 15: 5448-5460. PMID 31498621 DOI: 10.1021/acs.jctc.9b00473 |
0.199 |
|
| 2013 |
Liang C, Louhivuori M, Marrink SJ, Jansen TL, Knoester J. Vibrational Spectra of a Mechanosensitive Channel. The Journal of Physical Chemistry Letters. 4: 448-52. PMID 26281739 DOI: 10.1021/Jz3019258 |
0.198 |
|
| 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 |
0.196 |
|
| 2022 |
Ramírez-Palacios C, Marrink SJ. Computational prediction of ω-transaminase selectivity by deep learning analysis of molecular dynamics trajectories. Qrb Discovery. 4: e1. PMID 37529033 DOI: 10.1017/qrd.2022.22 |
0.193 |
|
| 2020 |
Vazquez-Salazar LI, Selle M, de Vries AH, Marrink SJ, Souza PCT. Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction Green Chemistry. 22: 7376-7386. DOI: 10.1039/d0gc01823f |
0.193 |
|
| 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 |
0.193 |
|
| 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 |
0.191 |
|
| 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 |
0.191 |
|
| 2010 |
Schafer LV, de Jong DH, Holt A, Rzepiela AJ, de Vries AH, Killian A, Marrink SJ. Sorting and Clustering of Transmembrane Helices in Coexisting Fluid Domains in Model Membranes Biophysical Journal. 98: 59a-60a. DOI: 10.1016/J.BPJ.2009.12.341 |
0.189 |
|
| 2001 |
Knackstedt MA, Marrink SJ, Sheppard AP, Pinczewski WV, Sahimi M. Transport in Porous Media. 44: 465-485. DOI: 10.1023/A:1010770010309 |
0.187 |
|
| 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 |
0.187 |
|
| 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 |
0.186 |
|
| 2013 |
Marrink SJ, Tieleman DP. Perspective on the Martini model. Chemical Society Reviews. 42: 6801-22. PMID 23708257 DOI: 10.1039/c3cs60093a |
0.186 |
|
| 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 |
0.186 |
|
| 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 |
0.183 |
|
| 2023 |
Chiariello MG, Grünewald F, Zarmiento-Garcia R, Marrink SJ. pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. The Journal of Physical Chemistry Letters. 905-911. PMID 36662680 DOI: 10.1021/acs.jpclett.2c03760 |
0.183 |
|
| 2014 |
Espinosa-Caballero MI, Periole X, de Vries A, Vargas-González MC, Marrink SJ, Ortega-Blake I, Carrillo-Tripp M. Amphotericin B Versus a Reduced Toxicity Chemical Analog in Aqueous and Lipid Media: An Md Comparative Study Biophysical Journal. 106: 802a. DOI: 10.1016/J.BPJ.2013.11.4397 |
0.174 |
|
| 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 |
0.174 |
|
| 2022 |
Sami S, Alessandri R, W Wijaya JB, Grünewald F, de Vries AH, Marrink SJ, Broer R, Havenith RWA. Strategies for Enhancing the Dielectric Constant of Organic Materials. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 126: 19462-19469. PMID 36425002 DOI: 10.1021/acs.jpcc.2c05682 |
0.172 |
|
| 2023 |
Thangaratnarajah C, Nijland M, Borges-Araújo L, Jeucken A, Rheinberger J, Marrink SJ, Souza PCT, Paulino C, Slotboom DJ. Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nature Communications. 14: 4484. PMID 37491368 DOI: 10.1038/s41467-023-40266-1 |
0.171 |
|
| 2023 |
Manrho M, Krishnaswamy SR, Kriete B, Patmanidis I, de Vries AH, Marrink SJ, Jansen TLC, Knoester J, Pshenichnikov MS. Watching Molecular Nanotubes Self-Assemble in Real Time. Journal of the American Chemical Society. 145: 22494-22503. PMID 37800477 DOI: 10.1021/jacs.3c07103 |
0.17 |
|
| 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 |
0.17 |
|
| 2017 |
Uusitalo JJ, Ingólfsson HI, Marrink SJ, Faustino I. Martini Coarse-Grained Force Field: Extension to RNA. Biophysical Journal. 113: 246-256. PMID 28633759 DOI: 10.1016/j.bpj.2017.05.043 |
0.169 |
|
| 2023 |
Ren M, Zhao L, Ma Z, An H, Marrink SJ, Sun F. Molecular basis of PIP2-dependent conformational switching of phosphorylated CD44 in binding FERM. Biophysical Journal. PMID 37218130 DOI: 10.1016/j.bpj.2023.05.021 |
0.169 |
|
| 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 |
0.164 |
|
| 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 |
0.162 |
|
| 2021 |
Alessandri R, Grünewald F, Marrink SJ. The Martini Model in Materials Science. Advanced Materials (Deerfield Beach, Fla.). 33: e2008635. PMID 33956373 DOI: 10.1002/adma.202008635 |
0.16 |
|
| 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 |
0.159 |
|
| 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 |
0.156 |
|
| 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 |
0.155 |
|
| 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 |
0.155 |
|
| 2023 |
Abraham Versloot RC, Arias-Orozco P, Tadema MJ, Rudolfus Lucas FL, Zhao X, Marrink SJ, Kuipers OP, Maglia G. Seeing the Invisibles: Detection of Peptide Enantiomers, Diastereomers, and Isobaric Ring Formation in Lanthipeptides Using Nanopores. Journal of the American Chemical Society. 145: 18355-18365. PMID 37579582 DOI: 10.1021/jacs.3c04076 |
0.154 |
|
| 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 |
0.154 |
|
| 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 |
0.154 |
|
| 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 |
0.152 |
|
| 2016 |
Liguori N, Periole X, Roy LM, Bot Y, Marrink SJ, Croce R. The Role of Protein Conformational Changes in Tuning the Fluorescence State of Light-Harvesting Complexes Biophysical Journal. 110: 313a. DOI: 10.1016/J.Bpj.2015.11.1683 |
0.146 |
|
| 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 |
0.146 |
|
| 2009 |
Baoukina S, Marrink SJ, Tieleman DP. Lateral Stress Profiles In Lipid Monolayers Biophysical Journal. 96: 159a. DOI: 10.1016/J.BPJ.2008.12.728 |
0.144 |
|
| 2015 |
Ingolfsson HI, Melo MN, Wassenaar TA, Periole X, de Vries AH, Tieleman DP, Marrink SJ. Computational Lipidomics and the Lipid Organization of Cell Envelopes Biophysical Journal. 108: 342a. DOI: 10.1016/J.BPJ.2014.11.1875 |
0.143 |
|
| 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 |
0.143 |
|
| 2022 |
Versloot RCA, Lucas FLR, Yakovlieva L, Tadema MJ, Zhang Y, Wood TM, Martin NI, Marrink SJ, Walvoort MTC, Maglia G. Quantification of Protein Glycosylation Using Nanopores. Nano Letters. PMID 35766994 DOI: 10.1021/acs.nanolett.2c01338 |
0.143 |
|
| 2016 |
Melo MN, Zavadlav J, Praprotnik M, Marrink SJ. Extending the Adress Multiscale Scheme for Protein and Bilayer Applications Biophysical Journal. 110: 643a-644a. DOI: 10.1016/J.BPJ.2015.11.3444 |
0.143 |
|
| 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 |
0.14 |
|
| 2021 |
Yakovlieva L, Ramírez-Palacios C, Marrink SJ, Walvoort MTC. Semiprocessive Hyperglycosylation of Adhesin by Bacterial Protein -Glycosyltransferases. Acs Chemical Biology. 16: 165-175. PMID 33401908 DOI: 10.1021/acschembio.0c00848 |
0.14 |
|
| 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 |
0.139 |
|
| 2023 |
Diamanti E, Souza PCT, Setyawati I, Bousis S, Gómez LM, Swier LJYM, Shams A, Tsarenko A, Stanek WK, Jäger M, Marrink SJ, Slotboom DJ, Hirsch AKH. Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications Biology. 6: 1182. PMID 37985798 DOI: 10.1038/s42003-023-05555-x |
0.134 |
|
| 2023 |
Gilbert BR, Thornburg ZR, Brier TA, Stevens JA, Grünewald F, Stone JE, Marrink SJ, Luthey-Schulten Z. Dynamics of chromosome organization in a minimal bacterial cell. Frontiers in Cell and Developmental Biology. 11: 1214962. PMID 37621774 DOI: 10.3389/fcell.2023.1214962 |
0.133 |
|
| 2020 |
Draper ER, Dietrich B, McAulay K, Brasnett C, Abdizadeh H, Patmanidis I, Marrink SJ, Su H, Cui H, Schweins R, Seddon A, Adams DJ. Using Small-Angle Scattering and Contrast Matching to Understand Molecular Packing in Low Molecular Weight Gels Matter. 2: 764-778. DOI: 10.1016/j.matt.2019.12.028 |
0.127 |
|
| 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 |
0.124 |
|
| 2024 |
Brown CM, Marrink SJ. Modeling membranes in situ. Current Opinion in Structural Biology. 87: 102837. PMID 38744147 DOI: 10.1016/j.sbi.2024.102837 |
0.12 |
|
| 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 |
0.12 |
|
| 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 |
0.118 |
|
| 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 |
0.117 |
|
| 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 |
0.117 |
|
| 2022 |
Losa J, Leupold S, Alonso-Martinez D, Vainikka P, Thallmair S, Tych KM, Marrink SJ, Heinemann M. Perspective: a stirring role for metabolism in cells. Molecular Systems Biology. 18: e10822. PMID 35362256 DOI: 10.15252/msb.202110822 |
0.112 |
|
| 2011 |
Risselada HJ, Marrink SJ, Müller M. Publisher’s Note: Curvature-Dependent Elastic Properties of Liquid-Ordered Domains Result in Inverted Domain Sorting on Uniaxially Compressed Vesicles [Phys. Rev. Lett.106, 148102 (2011)] Physical Review Letters. 106. DOI: 10.1103/PHYSREVLETT.106.169905 |
0.108 |
|
| 2023 |
Ramírez-Palacios C, Marrink SJ. Super High-Throughput Screening of Enzyme Variants by Spectral Graph Convolutional Neural Networks. Journal of Chemical Theory and Computation. PMID 36961994 DOI: 10.1021/acs.jctc.2c01227 |
0.107 |
|
| 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 |
0.105 |
|
| 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 |
0.1 |
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| 2020 |
Alessandri R, Sami S, Barnoud J, Vries AH, Marrink SJ, Havenith RWA. Resolving Donor–Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains Advanced Functional Materials. 30: 2004799. DOI: 10.1002/adfm.202004799 |
0.097 |
|
| 2018 |
Uusitalo JJ, Ingólfsson HI, Marrink SJ, Faustino I. Martini Coarse-Grained Force Field for RNA Biophysical Journal. 114: 437a. DOI: 10.1016/J.BPJ.2017.11.2416 |
0.097 |
|
| 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 |
0.093 |
|
| 2021 |
Marjanovic A, Ramírez-Palacios CJ, Masman MF, Drenth J, Otzen M, Marrink SJ, Janssen DB. Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase. Protein Engineering, Design & Selection : Peds. 34. PMID 34258615 DOI: 10.1093/protein/gzab016 |
0.088 |
|
| 2014 |
Yilmaz D, Konijnenberg A, Ingólfsson H, Dimitrova A, Marrink SJ, Sobott F, Koçer A. Following the Global Structural Changes of an Ion Channel During its Gating by using a Novel Mass Spectrometry Approach Biophysical Journal. 106: 554a. DOI: 10.1016/J.BPJ.2013.11.3083 |
0.088 |
|
| 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 |
0.086 |
|
| 2013 |
Arnarez C, Marrink SJ, Periole X. Erratum: Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels Scientific Reports. 3. DOI: 10.1038/srep01343 |
0.084 |
|
| 2022 |
Waclawiková B, Cesar Telles de Souza P, Schwalbe M, Neochoritis CG, Hoornenborg W, Nelemans SA, Marrink SJ, El Aidy S. Potential binding modes of the gut bacterial metabolite, 5-hydroxyindole, to the intestinal L-type calcium channels and its impact on the microbiota in rats. Gut Microbes. 15: 2154544. PMID 36511640 DOI: 10.1080/19490976.2022.2154544 |
0.083 |
|
| 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 |
0.083 |
|
| 2020 |
Dong L, Meng Q, Ramírez-Palacios C, Wijma HJ, Marrink SJ, Janssen DB. Asymmetric Synthesis of Optically Pure Aliphatic Amines with an Engineered Robust ω-Transaminase Catalysts. 10: 1310. DOI: 10.3390/catal10111310 |
0.083 |
|
| 2019 |
Piskorz TK, Gobbo C, Marrink SJ, De Feyter S, de Vries AH, van Esch JH. Nucleation Mechanisms of Self-Assembled Physisorbed Monolayers on Graphite The Journal of Physical Chemistry C. 123: 17510-17520. DOI: 10.1021/ACS.JPCC.9B01234 |
0.077 |
|
| 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 |
0.077 |
|
| 2011 |
Louhivuori M, Marrink SJ. Sensitivity of Coarse-Grained Mechano-Sensation Biophysical Journal. 100: 278a. DOI: 10.1016/j.bpj.2010.12.1727 |
0.076 |
|
| 2011 |
Westerbeek A, SzymaÅski 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 |
0.075 |
|
| 2017 |
Qiu L, Liu J, Alessandri R, Qiu X, Koopmans M, Havenith RA, Marrink SJ, Chiechi RC, Anton Koster LJ, Hummelen JC. Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics J. Mater. Chem. A. 5: 21234-21241. DOI: 10.1039/C7Ta06609K |
0.062 |
|
| 2024 |
Diamanti E, Souza PCT, Setyawati I, Bousis S, Monjas L, Swier LJYM, Shams A, Tsarenko A, Stanek WK, Jäger M, Marrink SJ, Slotboom DJ, Hirsch AKH. Author Correction: Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications Biology. 7: 70. PMID 38195913 DOI: 10.1038/s42003-024-05770-0 |
0.062 |
|
| 2016 |
de Jong DH, Baoukina S, Ingólfsson HI, Marrink SJ. Martini straight: Boosting performance using a shorter cutoff and GPUs Computer Physics Communications. 199: 1-7. DOI: 10.1016/j.cpc.2015.09.014 |
0.059 |
|
| 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 |
0.058 |
|
| 2014 |
Wassenaar TA, Pluhackova K, Böckmann R, Marrink SJ, Tieleman DP. Going Backward: An Efficient Multiscale Approach using Reverse Transformation Biophysical Journal. 106: 640a. DOI: 10.1016/J.BPJ.2013.11.3545 |
0.055 |
|
| 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 |
0.054 |
|
| 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 |
0.042 |
|
| 1999 |
Marrink SJ, Knackstedt MA. Percolation thresholds on elongated lattices Journal of Physics a: Mathematical and General. 32: L461-L466. DOI: 10.1088/0305-4470/32/44/101 |
0.041 |
|
| 2000 |
Marrink S, Paterson L, Knackstedt MA. Definition of percolation thresholds on self-affine surfaces Physica a: Statistical Mechanics and Its Applications. 280: 207-214. DOI: 10.1016/S0378-4371(99)00608-1 |
0.039 |
|
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