170 related articles for article (PubMed ID: 26617103)
1. Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact.
Florová P; Sklenovský P; Banáš P; Otyepka M
J Chem Theory Comput; 2010 Nov; 6(11):3569-79. PubMed ID: 26617103
[TBL] [Abstract][Full Text] [Related]
2. Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models.
Paschek D; Day R; García AE
Phys Chem Chem Phys; 2011 Nov; 13(44):19840-7. PubMed ID: 21845272
[TBL] [Abstract][Full Text] [Related]
3. Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models.
Zhang H; Yin C; Jiang Y; van der Spoel D
J Chem Inf Model; 2018 May; 58(5):1037-1052. PubMed ID: 29648448
[TBL] [Abstract][Full Text] [Related]
4. Protein simulations with an optimized water model: cooperative helix formation and temperature-induced unfolded state collapse.
Best RB; Mittal J
J Phys Chem B; 2010 Nov; 114(46):14916-23. PubMed ID: 21038907
[TBL] [Abstract][Full Text] [Related]
5. Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.
Vymetal J; Vondrásek J
J Phys Chem B; 2010 Apr; 114(16):5632-42. PubMed ID: 20361773
[TBL] [Abstract][Full Text] [Related]
6. Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.
Aliev AE; Courtier-Murias D
J Phys Chem B; 2010 Sep; 114(38):12358-75. PubMed ID: 20825228
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Temperature dependence of the hydrophobic hydration and interaction of simple solutes: an examination of five popular water models.
Paschek D
J Chem Phys; 2004 Apr; 120(14):6674-90. PubMed ID: 15267560
[TBL] [Abstract][Full Text] [Related]
9. Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied?
Nutt DR; Smith JC
J Chem Theory Comput; 2007 Jul; 3(4):1550-60. PubMed ID: 26633225
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. Predicting order and disorder for β-peptide foldamers in water.
Németh LJ; Hegedüs Z; Martinek TA
J Chem Inf Model; 2014 Oct; 54(10):2776-83. PubMed ID: 25177775
[TBL] [Abstract][Full Text] [Related]
12. Comparison of hydration behavior and conformational preferences of the Trp-cage mini-protein in different rigid-body water models.
Gupta M; Nayar D; Chakravarty C; Bandyopadhyay S
Phys Chem Chem Phys; 2016 Dec; 18(48):32796-32813. PubMed ID: 27878168
[TBL] [Abstract][Full Text] [Related]
13. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields.
Chen W; Shi C; MacKerell AD; Shen J
J Phys Chem B; 2015 Jun; 119(25):7902-10. PubMed ID: 26020564
[TBL] [Abstract][Full Text] [Related]
14. Are AMBER Force Fields and Implicit Solvation Models Additive? A Folding Study with a Balanced Peptide Test Set.
Robinson MK; Monroe JI; Shell MS
J Chem Theory Comput; 2016 Nov; 12(11):5631-5642. PubMed ID: 27731628
[TBL] [Abstract][Full Text] [Related]
15. Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations.
Cino EA; Choy WY; Karttunen M
J Chem Theory Comput; 2012 Aug; 8(8):2725-2740. PubMed ID: 22904695
[TBL] [Abstract][Full Text] [Related]
16. CHARMM TIP3P Water Model Suppresses Peptide Folding by Solvating the Unfolded State.
Boonstra S; Onck PR; Giessen Ev
J Phys Chem B; 2016 Apr; 120(15):3692-8. PubMed ID: 27031562
[TBL] [Abstract][Full Text] [Related]
17. Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model.
Nayar D; Chakravarty C
Phys Chem Chem Phys; 2014 Jun; 16(21):10199-213. PubMed ID: 24695799
[TBL] [Abstract][Full Text] [Related]
18. Dissecting the stability of a beta-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the beta-turn and beta-strand contributions to folding.
Griffiths-Jones SR; Maynard AJ; Searle MS
J Mol Biol; 1999 Oct; 292(5):1051-69. PubMed ID: 10512702
[TBL] [Abstract][Full Text] [Related]
19. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides.
Nerenberg PS; Head-Gordon T
J Chem Theory Comput; 2011 Apr; 7(4):1220-30. PubMed ID: 26606367
[TBL] [Abstract][Full Text] [Related]
20. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.
Shirts MR; Pande VS
J Chem Phys; 2005 Apr; 122(13):134508. PubMed ID: 15847482
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
