144 related articles for article (PubMed ID: 37352129)
1. Comparing the influence of explicit and implicit solvation models on site-specific thermodynamic stability of proteins.
Cho MK; Chong SH; Ham S; Shin S
J Comput Chem; 2023 Sep; 44(25):1976-1985. PubMed ID: 37352129
[TBL] [Abstract][Full Text] [Related]
2. Free energy landscape of protein folding in water: explicit vs. implicit solvent.
Zhou R
Proteins; 2003 Nov; 53(2):148-61. PubMed ID: 14517967
[TBL] [Abstract][Full Text] [Related]
3. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.
Roe DR; Okur A; Wickstrom L; Hornak V; Simmerling C
J Phys Chem B; 2007 Feb; 111(7):1846-57. PubMed ID: 17256983
[TBL] [Abstract][Full Text] [Related]
4. The effects of implicit modeling of nonpolar solvation on protein folding simulations.
Shao Q; Zhu W
Phys Chem Chem Phys; 2018 Jul; 20(27):18410-18419. PubMed ID: 29946610
[TBL] [Abstract][Full Text] [Related]
5. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.
Deng N; Zhang BW; Levy RM
J Chem Theory Comput; 2015 Jun; 11(6):2868-78. PubMed ID: 26236174
[TBL] [Abstract][Full Text] [Related]
6. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.
Katkova EV; Onufriev AV; Aguilar B; Sulimov VB
J Mol Graph Model; 2017 Mar; 72():70-80. PubMed ID: 28064081
[TBL] [Abstract][Full Text] [Related]
7. Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models.
Cumberworth A; Bui JM; Gsponer J
J Comput Chem; 2016 Mar; 37(7):629-40. PubMed ID: 26558440
[TBL] [Abstract][Full Text] [Related]
8. Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.
Anandakrishnan R; Izadi S; Onufriev AV
J Chem Theory Comput; 2019 Jan; 15(1):625-636. PubMed ID: 30514080
[TBL] [Abstract][Full Text] [Related]
9. Generalized Born Implicit Solvent Models for Biomolecules.
Onufriev AV; Case DA
Annu Rev Biophys; 2019 May; 48():275-296. PubMed ID: 30857399
[TBL] [Abstract][Full Text] [Related]
10. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.
Chen J; Brooks CL
Phys Chem Chem Phys; 2008 Jan; 10(4):471-81. PubMed ID: 18183310
[TBL] [Abstract][Full Text] [Related]
11. Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.
Izadi S; Aguilar B; Onufriev AV
J Chem Theory Comput; 2015 Sep; 11(9):4450-9. PubMed ID: 26575935
[TBL] [Abstract][Full Text] [Related]
12. Force field influences in beta-hairpin folding simulations.
Lwin TZ; Luo R
Protein Sci; 2006 Nov; 15(11):2642-55. PubMed ID: 17075138
[TBL] [Abstract][Full Text] [Related]
13. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.
Vorobjev YN; Almagro JC; Hermans J
Proteins; 1998 Sep; 32(4):399-413. PubMed ID: 9726412
[TBL] [Abstract][Full Text] [Related]
14. Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?
Zhou R; Berne BJ
Proc Natl Acad Sci U S A; 2002 Oct; 99(20):12777-82. PubMed ID: 12242327
[TBL] [Abstract][Full Text] [Related]
15. Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment.
Kent A; Jha AK; Fitzgerald JE; Freed KF
J Phys Chem B; 2008 May; 112(19):6175-86. PubMed ID: 18348560
[TBL] [Abstract][Full Text] [Related]
16. Computational protein design is a challenge for implicit solvation models.
Jaramillo A; Wodak SJ
Biophys J; 2005 Jan; 88(1):156-71. PubMed ID: 15377512
[TBL] [Abstract][Full Text] [Related]
17. Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins.
Shimizu S; Chan HS
Proteins; 2002 Jul; 48(1):15-30. PubMed ID: 12012334
[TBL] [Abstract][Full Text] [Related]
18. Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents.
Hua DP; Huang H; Roy A; Post CB
Protein Sci; 2016 Jan; 25(1):204-18. PubMed ID: 26189497
[TBL] [Abstract][Full Text] [Related]
19. Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations.
Lee MS; Olson MA
J Chem Phys; 2013 Jul; 139(4):044119. PubMed ID: 23901972
[TBL] [Abstract][Full Text] [Related]
20. Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model.
Rahimi AM; Jamali S; Bardhan JP; Lustig SR
J Chem Theory Comput; 2022 Sep; 18(9):5539-5558. PubMed ID: 36001344
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]