181 related articles for article (PubMed ID: 31751511)
1. pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model.
Miyazaki Y; Okazaki S; Shinoda W
J Chem Theory Comput; 2020 Jan; 16(1):782-793. PubMed ID: 31751511
[TBL] [Abstract][Full Text] [Related]
2. pSPICA Force Field Extended for Proteins and Peptides.
Miyazaki Y; Shinoda W
J Chem Inf Model; 2024 Jan; 64(2):532-542. PubMed ID: 38156656
[TBL] [Abstract][Full Text] [Related]
3. SPICA Force Field for Proteins and Peptides.
Kawamoto S; Liu H; Miyazaki Y; Seo S; Dixit M; DeVane R; MacDermaid C; Fiorin G; Klein ML; Shinoda W
J Chem Theory Comput; 2022 May; 18(5):3204-3217. PubMed ID: 35413197
[TBL] [Abstract][Full Text] [Related]
4. Improved prediction of bilayer and monolayer properties using a refined BMW-MARTINI force field.
Miguel V; Perillo MA; Villarreal MA
Biochim Biophys Acta; 2016 Nov; 1858(11):2903-2910. PubMed ID: 27591685
[TBL] [Abstract][Full Text] [Related]
5. SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol.
Seo S; Shinoda W
J Chem Theory Comput; 2019 Jan; 15(1):762-774. PubMed ID: 30514078
[TBL] [Abstract][Full Text] [Related]
6. Polarizable water model for the coarse-grained MARTINI force field.
Yesylevskyy SO; Schäfer LV; Sengupta D; Marrink SJ
PLoS Comput Biol; 2010 Jun; 6(6):e1000810. PubMed ID: 20548957
[TBL] [Abstract][Full Text] [Related]
7. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.
Hu Y; Sinha SK; Patel S
J Phys Chem B; 2014 Oct; 118(41):11973-92. PubMed ID: 25290376
[TBL] [Abstract][Full Text] [Related]
8. Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent.
Arnarez C; Uusitalo JJ; Masman MF; Ingólfsson HI; de Jong DH; Melo MN; Periole X; de Vries AH; Marrink SJ
J Chem Theory Comput; 2015 Jan; 11(1):260-75. PubMed ID: 26574224
[TBL] [Abstract][Full Text] [Related]
9. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes.
MacDermaid CM; Kashyap HK; DeVane RH; Shinoda W; Klauda JB; Klein ML; Fiorin G
J Chem Phys; 2015 Dec; 143(24):243144. PubMed ID: 26723629
[TBL] [Abstract][Full Text] [Related]
10. The importance of membrane defects-lessons from simulations.
Bennett WF; Tieleman DP
Acc Chem Res; 2014 Aug; 47(8):2244-51. PubMed ID: 24892900
[TBL] [Abstract][Full Text] [Related]
11. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.
Wassenaar TA; Ingólfsson HI; Priess M; Marrink SJ; Schäfer LV
J Phys Chem B; 2013 Apr; 117(13):3516-30. PubMed ID: 23406326
[TBL] [Abstract][Full Text] [Related]
12. A Practical View of the Martini Force Field.
Bruininks BMH; Souza PCT; Marrink SJ
Methods Mol Biol; 2019; 2022():105-127. PubMed ID: 31396901
[TBL] [Abstract][Full Text] [Related]
13. Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system.
Riniker S; van Gunsteren WF
J Chem Phys; 2012 Jul; 137(4):044120. PubMed ID: 22852610
[TBL] [Abstract][Full Text] [Related]
14. Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study.
Miyazaki Y; Shinoda W
Biochim Biophys Acta Biomembr; 2022 Sep; 1864(9):183955. PubMed ID: 35526599
[TBL] [Abstract][Full Text] [Related]
15. Extension of CAVS coarse-grained model to phospholipid membranes: The importance of electrostatics.
Shen H; Deng M; Zhang Y
J Comput Chem; 2017 May; 38(13):971-980. PubMed ID: 28266037
[TBL] [Abstract][Full Text] [Related]
16. Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field.
Shinoda W; DeVane R; Klein ML
J Phys Chem B; 2010 May; 114(20):6836-49. PubMed ID: 20438090
[TBL] [Abstract][Full Text] [Related]
17. Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: difference between atomistic and coarse-grained simulations.
Nishizawa M; Nishizawa K
J Chem Phys; 2014 Aug; 141(7):075101. PubMed ID: 25149815
[TBL] [Abstract][Full Text] [Related]
18. Development of Coarse-Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm.
Wan M; Song J; Li W; Gao L; Fang W
J Comput Chem; 2020 Mar; 41(8):814-829. PubMed ID: 31859392
[TBL] [Abstract][Full Text] [Related]
19. Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics.
Hu Y; Sinha SK; Patel S
Langmuir; 2015 Jun; 31(24):6615-31. PubMed ID: 25614183
[TBL] [Abstract][Full Text] [Related]
20. Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A.
Yoo J; Cui Q
Biophys J; 2013 Jan; 104(1):117-27. PubMed ID: 23332064
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
