| 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 |