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refs.bib
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@article{javanainen23,
author = {Javanainen, Matti and Heftberger, Peter and Madsen, Jesper J. and Miettinen, Markus S. and Pabst, Georg and Ollila, O. H. Samuli},
title = {Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions},
journal = {Journal of Chemical Theory and Computation},
volume = {19},
number = {18},
pages = {6342-6352},
year = {2023},
}
@article{mobley18,
author = {Mobley, David L. and Bannan, Caitlin C. and Rizzi, Andrea and Bayly, Christopher I. and Chodera, John D. and Lim, Victoria T. and Lim, Nathan M. and Beauchamp, Kyle A. and Slochower, David R. and Shirts, Michael R. and Gilson, Michael K. and Eastman, Peter
K.},
title = {Escaping Atom Types in Force Fields Using Direct Chemical Perception},
journal = {Journal of Chemical Theory and Computation},
volume = {14},
number = {11},
pages = {6076-6092},
year = {2018},
}
@article{boothroyd23,
author = {Boothroyd, Simon and Behara, Pavan Kumar and Madin, Owen C. and Hahn, David F. and Jang, Hyesu and Gapsys, Vytautas and Wagner, Jeffrey R. and Horton, Joshua T. and Dotson, David L. and Thompson, Matthew W. and Maat, Jessica and Gokey, Trevor and Wang, Lee-Ping and Cole, Daniel J. and Gilson, Michael K. and Chodera, John D. and Bayly, Christopher I. and Shirts, Michael R. and Mobley, David L.},
title = {Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field},
journal = {Journal of Chemical Theory and Computation},
volume = {19},
number = {11},
pages = {3251-3275},
year = {2023},
}
@misc{OpenFFgit,
title = {Openff-interchange},
howpublished = {\url{https://zenodo.org/doi/10.5281/zenodo.8147764}},
note = {Accessed: 2013-10-21}
}
@misc{NMRlipidsExperimentalData,
title = {Adding experimental data into the NMRlipids databank},
howpublished = {\url{https://nmrlipids.github.io/addingExpData.html}},
note = {Accessed: 2013-10-10}
}
@misc{NMRlipidsREADMEfiles,
title = {User input and content of README.yaml files},
howpublished = {\url{https://nmrlipids.github.io/READMEcontent.html}},
note = {Accessed: 2013-10-10}
}
@misc{NMRlipidsExampleAndTutorials,
title = {Examples and tutorials for using the NMRlipids databank},
howpublished = {\url{https://nmrlipids.github.io/exampleAndTutorials.html}},
note = {Accessed: 2013-10-10}
}
@misc{NMRlipidsDocsMolAndMapping,
title = {Universal molecule and atom names in the NMRlipids databank},
howpublished = {\url{https://nmrlipids.github.io/moleculesAndMapping.html}},
note = {Accessed: 2013-10-10}
}
@article{shahane19,
author={Shahane, Ganesh
and Ding, Wei
and Palaiokostas, Michail
and Orsi, Mario},
title={Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations},
journal={Journal of Molecular Modeling},
year={2019},
month={Feb},
day={26},
volume={25},
number={3},
pages={76},
}
@article{kumar21,
title = {Study of lipid heterogeneity on bilayer membranes using molecular dynamics simulations},
journal = {Journal of Molecular Graphics and Modelling},
volume = {108},
pages = {108000},
year = {2021},
issn = {1093-3263},
url = {https://www.sciencedirect.com/science/article/pii/S1093326321001716},
author = {Nandan Kumar and G. Narahari Sastry},
}
@article{oliveira22,
AUTHOR = {Oliveira, Aline A. and Róg, Tomasz and da Silva, Albérico B. F. and Amaro, Rommie E. and Johnson, Mark S. and Postila, Pekka A.},
TITLE = {Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations},
JOURNAL = {Biomolecules},
VOLUME = {12},
YEAR = {2022},
NUMBER = {2},
ARTICLE-NUMBER = {183},
}
@article{ivanova15,
author = {Ivanova, Pavlina T. and Myers, David S. and Milne, Stephen B. and McClaren, Jennifer L. and Thomas, Paul G. and Brown, H. Alex},
title = {Lipid Composition of the Viral Envelope of Three Strains of Influenza Virus—Not All Viruses Are Created Equal},
journal = {ACS Infectious Diseases},
volume = {1},
number = {9},
pages = {435-442},
year = {2015},
}
@article{gerl12,
author = {Gerl, Mathias J. and Sampaio, Julio L. and Urban, Severino and Kalvodova, Lucie and Verbavatz, Jean-Marc and Binnington, Beth and Lindemann, Dirk and Lingwood, Clifford A. and Shevchenko, Andrej and Schroeder, Cornelia and Simons, Kai},
title = "{Quantitative analysis of the lipidomes of the influenza virus envelope and MDCK cell apical membrane}",
journal = {Journal of Cell Biology},
volume = {196},
number = {2},
pages = {213-221},
year = {2012},
month = {01},
}
@article{binotti21,
title = {An overview of the synaptic vesicle lipid composition},
journal = {Archives of Biochemistry and Biophysics},
volume = {709},
pages = {108966},
year = {2021},
issn = {0003-9861},
doi = {https://doi.org/10.1016/j.abb.2021.108966},
url = {https://www.sciencedirect.com/science/article/pii/S0003986121002150},
author = {Beyenech Binotti and Reinhard Jahn and Ángel Pérez-Lara},
}
@article{chwastek20,
title = {Principles of Membrane Adaptation Revealed through Environmentally Induced Bacterial Lipidome Remodeling},
journal = {Cell Reports},
volume = {32},
number = {12},
pages = {108165},
year = {2020},
issn = {2211-1247},
doi = {https://doi.org/10.1016/j.celrep.2020.108165},
url = {https://www.sciencedirect.com/science/article/pii/S2211124720311542},
author = {Grzegorz Chwastek and Michal A. Surma and Sandra Rizk and Daniel Grosser and Oksana Lavrynenko and Magdalena Rucińska and Helena Jambor and James Sáenz},
}
@Article{casares19,
AUTHOR = {Casares, Doralicia and Escribá, Pablo V. and Rosselló, Catalina Ana},
TITLE = {Membrane Lipid Composition: Effect on Membrane and Organelle Structure, Function and Compartmentalization and Therapeutic Avenues},
JOURNAL = {International Journal of Molecular Sciences},
VOLUME = {20},
YEAR = {2019},
NUMBER = {9},
ARTICLE-NUMBER = {2167},
}
@article{escriba15,
title = {Membrane lipid therapy: Modulation of the cell membrane composition and structure as a molecular base for drug discovery and new disease treatment},
journal = {Progress in Lipid Research},
volume = {59},
pages = {38-53},
year = {2015},
issn = {0163-7827},
doi = {https://doi.org/10.1016/j.plipres.2015.04.003},
url = {https://www.sciencedirect.com/science/article/pii/S0163782715000247},
author = {Pablo V. Escribá and Xavier Busquets and Jin-ichi Inokuchi and Gábor Balogh and Zsolt Török and Ibolya Horváth and John L. Harwood and László Vígh},
}
@article{doktorova20,
author = {Doktorova, Milka and Kučerka, Norbert and Kinnun, Jacob J. and Pan, Jianjun and Marquardt, Drew and Scott, Haden L. and Venable, Richard M. and Pastor, Richard W. and Wassall, Stephen R. and Katsaras, John and Heberle, Frederick A.},
title = {Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data},
journal = {The Journal of Physical Chemistry B},
volume = {124},
number = {25},
pages = {5186-5200},
year = {2020},
}
@article{hanashima19,
title = {Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup},
journal = {Biophysical Journal},
volume = {117},
number = {2},
pages = {307-318},
year = {2019},
issn = {0006-3495},
doi = {https://doi.org/10.1016/j.bpj.2019.06.019},
url = {https://www.sciencedirect.com/science/article/pii/S0006349519305089},
author = {Shinya Hanashima and Kazuhiro Murakami and Michihiro Yura and Yo Yano and Yuichi Umegawa and Hiroshi Tsuchikawa and Nobuaki Matsumori and Sangjae Seo and Wataru Shinoda and Michio Murata},
}
@article{Tiemann23,
title={MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations}, url={http://dx.doi.org/10.7554/eLife.90061.1}, DOI={10.7554/elife.90061.1}, publisher={eLife Sciences Publications, Ltd}, author={Tiemann, Johanna K. S. and Szczuka, Magdalena and Bouarroudj, Lisa and Oussaren, Mohamed and Garcia, Steven and Howard, Rebecca J. and Delemotte, Lucie and Lindahl, Erik and Baaden, Marc and Lindorff-Larsen, Kresten and Chavent, Matthieu and Poulain, Pierre}, year={2023}, month=sep }
@Article{sever23,
author={Sever, Richard},
title={We need a plan D},
journal={Nature Methods},
year={2023},
month={Apr},
day={01},
volume={20},
number={4},
pages={473-474},
issn={1548-7105},
doi={10.1038/s41592-023-01817-y},
url={https://doi.org/10.1038/s41592-023-01817-y}
}
@Article{NatMethEdit23,
title={Data sharing is the future},
journal={Nature Methods},
year={2023},
month={Apr},
day={01},
volume={20},
number={4},
pages={471-471},
abstract={We examine data sharing practices and explore possible future directions.},
issn={1548-7105},
doi={10.1038/s41592-023-01865-4},
url={https://doi.org/10.1038/s41592-023-01865-4}
}
@software{DatabankZenodo,
author = {A. Kiirikki and others},
title = {{NMRLipids Databank}},
month = apr,
year = 2023,
publisher = {Zenodo},
version = {v1.0.0},
doi = {10.5281/zenodo.7875568},
url = {https://doi.org/10.5281/zenodo.7875568}
}
@article{lin23,
author = {Zeming Lin and Halil Akin and Roshan Rao and Brian Hie and Zhongkai Zhu and Wenting Lu and Nikita Smetanin and Robert Verkuil and Ori Kabeli and Yaniv Shmueli and Allan dos Santos Costa and Maryam Fazel-Zarandi and Tom Sercu and Salvatore Candido and Alexander Rives },
title = {Evolutionary-scale prediction of atomic-level protein structure with a language model},
journal = {Science},
volume = {379},
number = {6637},
pages = {1123-1130},
year = {2023},
doi = {10.1126/science.ade2574},
URL = {https://www.science.org/doi/abs/10.1126/science.ade2574},
eprint = {https://www.science.org/doi/pdf/10.1126/science.ade2574},
}
@article{baek21,
author = {Minkyung Baek and Frank DiMaio and Ivan Anishchenko and Justas Dauparas and Sergey Ovchinnikov and Gyu Rie Lee and Jue Wang and Qian Cong and Lisa N. Kinch and R. Dustin Schaeffer and Claudia Millán and Hahnbeom Park and Carson Adams and Caleb R. Glassman and Andy DeGiovanni and Jose H. Pereira and Andria V. Rodrigues and Alberdina A. van Dijk and Ana C. Ebrecht and Diederik J. Opperman and Theo Sagmeister and Christoph Buhlheller and Tea Pavkov-Keller and Manoj K. Rathinaswamy and Udit Dalwadi and Calvin K. Yip and John E. Burke and K. Christopher Garcia and Nick V. Grishin and Paul D. Adams and Randy J. Read and David Baker },
title = {Accurate prediction of protein structures and interactions using a three-track neural network},
journal = {Science},
volume = {373},
number = {6557},
pages = {871-876},
year = {2021},
doi = {10.1126/science.abj8754},
URL = {https://www.science.org/doi/abs/10.1126/science.abj8754},
eprint = {https://www.science.org/doi/pdf/10.1126/science.abj8754},
}
@article{wur23,
author = {Wurl, Anika and M. Ferreira, Tiago},
title = {Atomistic MD Simulations of n-Alkanes in a Phospholipid Bilayer: CHARMM36 versus Slipids},
journal = {Macromolecular Theory and Simulations},
volume = {32},
number = {3},
pages = {2200078},
keywords = {alkanes, CHARMM36, lipid membranes, molecular dynamic simulations, Slipids},
doi = {https://doi.org/10.1002/mats.202200078},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mats.202200078},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/mats.202200078},
year = {2023}
}
@article{klukowski22,
author={Klukowski, Piotr
and Riek, Roland
and G{\"u}ntert, Peter},
title={Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA},
journal={Nat. Commun.},
year={2022},
month={Oct},
day={18},
volume={13},
number={1},
pages={6151},
}
@article{roos19,
author = {Roos, Katarina and Wu, Chuanjie and Damm, Wolfgang and Reboul, Mark and Stevenson, James M. and Lu, Chao and Dahlgren, Markus K. and Mondal, Sayan and Chen, Wei and Wang, Lingle and Abel, Robert and Friesner, Richard A. and Harder, Edward D.},
title = {OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules},
journal = {Journal of Chemical Theory and Computation},
volume = {15},
number = {3},
pages = {1863-1874},
year = {2019},
}
@mastersthesis{nencini2019development,
title={ Development and testing of computer models of phospholipid membranes.},
author={Nencini, Ricky},
year={2019},
school={Charles University of Prague},
doi={http://hdl.handle.net/20.500.11956/106127},
note={http://hdl.handle.net/20.500.11956/106127}
}
@article{ermilova16,
author = {Ermilova, Inna and Lyubartsev, Alexander P.},
title = {Extension of the Slipids Force Field to Polyunsaturated Lipids},
journal = {The Journal of Physical Chemistry B},
volume = {120},
number = {50},
pages = {12826-12842},
year = {2016},
}
@article{Slatter:2016a,
author = {Slatter, David A. and Aldrovandi, Maceler and O'Connor, Anne and Allen, Stuart M. and Brasher, Christopher J. and Murphy, Robert C. and Mecklemann, Sven and Ravi, Saranya and Darley-Usmar, Victor and O'Donnell, Valerie B.},
journal = {Cell Metab.},
pages = {930--944},
title = {{Mapping the {Human} {Platelet} {Lipidome} {Reveals} {Cytosolic} {Phospholipase} {A2} as a {Regulator} of {Mitochondrial} {Bioenergetics} during {Activation}}},
volume = {23},
year = {2016}}
@article{Lorent:2020a,
author = {Lorent, J. H. and Levental, K. R. and Ganesan, L. and Rivera-Longsworth, G. and Sezgin, E. and Doktorova, M. and Lyman, E. and Levental, I.},
journal = {Nat. Chem. Biol.},
pages = {644--652},
title = {{Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape}},
volume = {16},
year = {2020}}
@article{santuz21,
url = {https://doi.org/10.21105/joss.03521},
year = {2021},
publisher = {The Open Journal},
volume = {6},
number = {65},
pages = {3521},
author = {Hubert Santuz and Amélie Bacle and Pierre Poulain and Patrick F.j. Fuchs},
title = {buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters},
journal = {Journal of Open Source Software}
}
@article{grote20,
author = {Grote, Fredrik and Lyubartsev, Alexander P.},
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address = {New York, NY, USA},
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doi = {10.1145/3458817.3487397},
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pages = {1-11},
location = {St. Louis, Missouri},
series = {SC '21}
}
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