Limonada - References

Name	Title	Year
West2020	How Do Ethanolamine Plasmalogens Contribute to Order and Structure of Neurological Membranes? West Ana, Zoni Valeria, Teague Walter E., Leonard Alison N., Vanni Stefano, Gawrisch Klaus, Tristram-Nagle Stephanie, Sachs Jonathan N., Klauda Jeffery B. The Journal of Physical Chemistry B, 2020, 124. DOI: 10.1021/acs.jpcb.9b08850	2020
Adams2018	Simulations of simple Bovine and Homo sapiens outer cortex ocular lens membrane models with a majority concentration of cholesterol Adams Mark, Wang Eric, Zhuang Xiaohong, Klauda Jeffery B. Biochimica et Biophysica Acta (BBA) - Biomembranes, 2018, 1860. DOI: 10.1016/j.bbamem.2017.11.010	2018
Wang2018a	Simulations of Pure Ceramide and Ternary Lipid Mixtures as Simple Interior Stratum Corneum Models Wang Eric, Klauda Jeffery B. The Journal of Physical Chemistry B, 2018, 122. DOI: 10.1021/acs.jpcb.8b00348	2018
Yu2018	Modeling Pseudomonas aeruginosa inner plasma membrane in planktonic and biofilm modes Yu Yalun, Klauda Jeffery B. The Journal of Chemical Physics, 2018, 149. DOI: 10.1063/1.5052629	2018
Wang2018b	Models for the Stratum Corneum Lipid Matrix: Effects of Ceramide Concentration, Ceramide Hydroxylation, and Free Fatty Acid Protonation Wang Eric, Klauda Jeffery B. The Journal of Physical Chemistry B, 2018, 122. DOI: 10.1021/acs.jpcb.8b06188	2018
Leonard2018	Parameterization of the CHARMM All-Atom Force Field for Ether Lipids and Model Linear Ethers Leonard Alison N., Pastor Richard W., Klauda Jeffery B. The Journal of Physical Chemistry B, 2018, 122. DOI: 10.1021/acs.jpcb.8b02743	2018
Emami2017	Molecular dynamics simulations of ternary lipid bilayers containing plant sterol and glucosylceramide Emami Shiva, Azadmard-Damirchi Sodeif, Peighambardoust Seyed Hadi, Hesari Javad, Valizadeh Hadi, Faller Roland Chemistry and Physics of Lipids, 2017, 203. DOI: 10.1016/j.chemphyslip.2017.01.003	2017
Zhuang2017	Simulations of simple linoleic acid-containing lipid membranes and models for the soybean plasma membranes Zhuang Xiaohong, Ou Anna, Klauda Jeffery B. The Journal of Chemical Physics, 2017, 146. DOI: 10.1063/1.4983655	2017
Ingólfsson2017	Computational Lipidomics of the Neuronal Plasma Membrane Ingólfsson Helgi I., Carpenter Timothy S., Bhatia Harsh, Bremer Peer-Timo, Marrink Siewert J., Lightstone Felice C. Biophysical Journal, 2017, 113. DOI: 10.1016/j.bpj.2017.10.017	2017
Ma2017	Modeling Diversity in Structures of Bacterial Outer Membrane Lipids Ma Huilin, Cummins Daniel D., Edelstein Natalie Brooke, Gomez Jerry, Khan Aliza, Llewellyn Masud Dikita, Picudella Tara, Willsey Sarah Rose, Nangia Shikha Journal of Chemical Theory and Computation, 2017, 13. DOI: 10.1021/acs.jctc.6b00856	2017
Ermilova2016	Extension of the Slipids Force Field to Polyunsaturated Lipids Ermilova Inna, Lyubartsev Alexander P. The Journal of Physical Chemistry B, 2016, 120. DOI: 10.1021/acs.jpcb.6b05422	2016
Gu2016	Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations Gu Ruo-Xu, Ingólfsson Helgi I., de Vries Alex H., Marrink Siewert J., Tieleman D. Peter The Journal of Physical Chemistry B, 2016, 121. DOI: 10.1021/acs.jpcb.6b07142	2016
Róg2016	Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters Róg Tomasz, Orłowski Adam, Llorente Alicia, Skotland Tore, Sylvänne Tuulia, Kauhanen Dimple, Ekroos Kim, Sandvig Kirsten, Vattulainen Ilpo Data in Brief, 2016, 7. DOI: 10.1016/j.dib.2016.03.067	2016
Wassenaar2015	Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations Wassenaar Tsjerk A., Ingólfsson Helgi I., Böckmann Rainer A., Tieleman D. Peter, Marrink Siewert J. Journal of Chemical Theory and Computation, 2015, 11. DOI: 10.1021/acs.jctc.5b00209	2015
Lee2015	CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field Lee Jumin, Cheng Xi, Swails Jason M., Yeom Min Sun, Eastman Peter K., Lemkul Justin A., Wei Shuai, Buckner Joshua, Jeong Jong Cheol, Qi Yifei, Jo Sunhwan, Pande Vijay S., Case David A., Brooks Charles L., MacKerell Alexander D., Klauda Jeffery B., Im Wonpil Journal of Chemical Theory and Computation, 2015, 12. DOI: 10.1021/acs.jctc.5b00935	2015
vanEerden2015	Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations van Eerden Floris J., de Jong Djurre H., de Vries Alex H., Wassenaar Tsjerk A., Marrink Siewert J. Biochimica et Biophysica Acta (BBA) - Biomembranes, 2015, 1848. DOI: 10.1016/j.bbamem.2015.02.025	2015
Melo2015	Parameters for Martini sterols and hopanoids based on a virtual-site description Melo M. N., Ingólfsson H. I., Marrink S. J. The Journal of Chemical Physics, 2015, 143. DOI: 10.1063/1.4937783	2015
Monje-Galvan2015	Modeling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties Monje-Galvan Viviana, Klauda Jeffery B. Biochemistry, 2015, 54. DOI: 10.1021/acs.biochem.5b00718	2015
Róg2015	Interdigitation of long-chain sphingomyelin induces coupling of membrane leaflets in a cholesterol dependent manner Róg Tomasz, Orłowski Adam, Llorente Alicia, Skotland Tore, Sylvänne Tuulia, Kauhanen Dimple, Ekroos Kim, Sandvig Kirsten, Vattulainen Ilpo Biochimica et Biophysica Acta (BBA) - Biomembranes, 2015, 1858. DOI: 10.1016/j.bbamem.2015.12.003	2015
Kulig2015	Cis and trans unsaturated phosphatidylcholine bilayers: A molecular dynamics simulation study Kulig Waldemar, Pasenkiewicz-Gierula Marta, Róg T. Chemistry and Physics of Lipids, 2015, 195. DOI: 10.1016/j.chemphyslip.2015.07.002	2015
Kulig2015b	Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol Kulig Waldemar, Pasenkiewicz-Gierula Marta, Róg Tomasz Data in Brief, 2015, 5. DOI: 10.1016/j.dib.2015.09.013	2015
Wu2014	CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations Wu Emilia L., Cheng Xi, Jo Sunhwan, Rui Huan, Song Kevin C., Dávila-Contreras Eder M., Qi Yifei, Lee Jumin, Monje-Galvan Viviana, Venable Richard M., Klauda Jeffery B., Im Wonpil Journal of Computational Chemistry, 2014, 35. DOI: 10.1002/jcc.23702	2014
Venable2014	CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature Venable Richard M., Sodt Alexander J., Rogaski Brent, Rui Huan, Hatcher Elizabeth, MacKerell Alexander D., Pastor Richard W., Klauda Jeffery B. Biophysical Journal, 2014, 107. DOI: 10.1016/j.bpj.2014.05.034	2014
Ingólfsson2014	Lipid Organization of the Plasma Membrane Ingólfsson Helgi I., Melo Manuel N., van Eerden Floris J., Arnarez Clément, Lopez Cesar A., Wassenaar Tsjerk A., Periole Xavier, de Vries Alex H., Tieleman D. Peter, Marrink Siewert J. Journal of the American Chemical Society, 2014, 136. DOI: 10.1021/ja507832e	2014
Maciejewski2014	Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration Maciejewski Arkadiusz, Pasenkiewicz-Gierula Marta, Cramariuc Oana, Vattulainen Ilpo, Rog Tomasz The Journal of Physical Chemistry B, 2014, 118. DOI: 10.1021/jp5016627	2014

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