235 related articles for article (PubMed ID: 35793442)
1. Transferable and Polarizable Coarse Grained Model for Proteins─ProMPT.
Sahoo A; Lee PY; Matysiak S
J Chem Theory Comput; 2022 Aug; 18(8):5046-5055. PubMed ID: 35793442
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.
Frembgen-Kesner T; Andrews CT; Li S; Ngo NA; Shubert SA; Jain A; Olayiwola OJ; Weishaar MR; Elcock AH
J Chem Theory Comput; 2015 May; 11(5):2341-54. PubMed ID: 26574429
[TBL] [Abstract][Full Text] [Related]
4. Flexible Boundaries for Multiresolution Solvation: An Algorithm for Spatial Multiscaling in Molecular Dynamics Simulations.
Szklarczyk OM; Bieler NS; Hünenberger PH; van Gunsteren WF
J Chem Theory Comput; 2015 Nov; 11(11):5447-63. PubMed ID: 26574333
[TBL] [Abstract][Full Text] [Related]
5. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.
Rzepiela AJ; Louhivuori M; Peter C; Marrink SJ
Phys Chem Chem Phys; 2011 Jun; 13(22):10437-48. PubMed ID: 21494747
[TBL] [Abstract][Full Text] [Related]
6. Translocation thermodynamics of linear and cyclic nonaarginine into model DPPC bilayer via coarse-grained molecular dynamics simulation: implications of pore formation and nonadditivity.
Hu Y; Liu X; Sinha SK; Patel S
J Phys Chem B; 2014 Mar; 118(10):2670-82. PubMed ID: 24506488
[TBL] [Abstract][Full Text] [Related]
7. Procedure for Transferable Coarse-Grained Models of Aqueous Polysaccharides.
Sauter J; Grafmüller A
J Chem Theory Comput; 2017 Jan; 13(1):223-236. PubMed ID: 27997210
[TBL] [Abstract][Full Text] [Related]
8. Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins.
Li M; Zhang JZ
Phys Chem Chem Phys; 2017 Mar; 19(10):7410-7419. PubMed ID: 28244513
[TBL] [Abstract][Full Text] [Related]
9. Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations.
Riniker S; Eichenberger AP; van Gunsteren WF
Eur Biophys J; 2012 Aug; 41(8):647-61. PubMed ID: 22797564
[TBL] [Abstract][Full Text] [Related]
10. Multiscale coarse-graining of the protein energy landscape.
Hills RD; Lu L; Voth GA
PLoS Comput Biol; 2010 Jun; 6(6):e1000827. PubMed ID: 20585614
[TBL] [Abstract][Full Text] [Related]
11. A transferable coarse-grained model for diphenylalanine: how to represent an environment driven conformational transition.
Dalgicdir C; Sensoy O; Peter C; Sayar M
J Chem Phys; 2013 Dec; 139(23):234115. PubMed ID: 24359360
[TBL] [Abstract][Full Text] [Related]
12. The CUMULUS coarse graining method: transferable potentials for water and solutes.
van Hoof B; Markvoort AJ; van Santen RA; Hilbers PA
J Phys Chem B; 2011 Aug; 115(33):10001-12. PubMed ID: 21740053
[TBL] [Abstract][Full Text] [Related]
13. Protein simulation using coarse-grained two-bead multipole force field with polarizable water models.
Li M; Zhang JZ
J Chem Phys; 2017 Feb; 146(6):065101. PubMed ID: 28201893
[TBL] [Abstract][Full Text] [Related]
14. Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase.
Eichenberger AP; Huang W; Riniker S; van Gunsteren WF
J Chem Theory Comput; 2015 Jul; 11(7):2925-37. PubMed ID: 26575730
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation.
Villa A; Peter C; van der Vegt NF
Phys Chem Chem Phys; 2009 Mar; 11(12):2077-86. PubMed ID: 19280018
[TBL] [Abstract][Full Text] [Related]
17. TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.
Li M; Liu F; Zhang JZ
J Chem Theory Comput; 2016 Dec; 12(12):6147-6156. PubMed ID: 27782390
[TBL] [Abstract][Full Text] [Related]
18. Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field.
Plazinski W; Lutsyk V; Plazinska A
J Chem Theory Comput; 2024 Mar; 20(5):2273-2283. PubMed ID: 38427574
[TBL] [Abstract][Full Text] [Related]
19. Transferability of coarse-grained force fields: the polymer case.
Carbone P; Varzaneh HA; Chen X; Müller-Plathe F
J Chem Phys; 2008 Feb; 128(6):064904. PubMed ID: 18282071
[TBL] [Abstract][Full Text] [Related]
20. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.
Andrews CT; Elcock AH
J Chem Theory Comput; 2014 Nov; 10(11):5178-5194. PubMed ID: 25400526
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]