293 related articles for article (PubMed ID: 22904695)
1. 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]
2. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.
Watts CR; Gregory A; Frisbie C; Lovas S
Proteins; 2018 Mar; 86(3):279-300. PubMed ID: 29235155
[TBL] [Abstract][Full Text] [Related]
3. Critical Assessment of Current Force Fields. Short Peptide Test Case.
Vymětal J; Vondrášek J
J Chem Theory Comput; 2013 Jan; 9(1):441-51. PubMed ID: 26589046
[TBL] [Abstract][Full Text] [Related]
4. Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models.
Ge Y; Kier BL; Andersen NH; Voelz VA
J Chem Inf Model; 2017 Jul; 57(7):1609-1620. PubMed ID: 28614661
[TBL] [Abstract][Full Text] [Related]
5. An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides.
Maffucci I; Contini A
J Chem Theory Comput; 2016 Feb; 12(2):714-27. PubMed ID: 26784558
[TBL] [Abstract][Full Text] [Related]
6. Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.
Beauchamp KA; Lin YS; Das R; Pande VS
J Chem Theory Comput; 2012 Apr; 8(4):1409-1414. PubMed ID: 22754404
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Dynamic properties of force fields.
Vitalini F; Mey AS; Noé F; Keller BG
J Chem Phys; 2015 Feb; 142(8):084101. PubMed ID: 25725706
[TBL] [Abstract][Full Text] [Related]
9. Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics.
Pantelopulos GA; Mukherjee S; Voelz VA
Proteins; 2015 Sep; 83(9):1665-76. PubMed ID: 26138282
[TBL] [Abstract][Full Text] [Related]
10. Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.
Kundu S
J Biomol Struct Dyn; 2018 Feb; 36(2):302-317. PubMed ID: 28024449
[TBL] [Abstract][Full Text] [Related]
11. The Dependence of Amyloid-β Dynamics on Protein Force Fields and Water Models.
Somavarapu AK; Kepp KP
Chemphyschem; 2015 Oct; 16(15):3278-89. PubMed ID: 26256268
[TBL] [Abstract][Full Text] [Related]
12. Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields.
Meher BR; Kumar MV; Sharma S; Bandyopadhyay P
J Bioinform Comput Biol; 2012 Dec; 10(6):1250018. PubMed ID: 22845837
[TBL] [Abstract][Full Text] [Related]
13. Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models.
Xu L; Sun H; Li Y; Wang J; Hou T
J Phys Chem B; 2013 Jul; 117(28):8408-21. PubMed ID: 23789789
[TBL] [Abstract][Full Text] [Related]
14. Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Lindorff-Larsen K; Piana S; Palmo K; Maragakis P; Klepeis JL; Dror RO; Shaw DE
Proteins; 2010 Jun; 78(8):1950-8. PubMed ID: 20408171
[TBL] [Abstract][Full Text] [Related]
15. Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields.
Gopal SM; Wingbermühle S; Schnatwinkel J; Juber S; Herrmann C; Schäfer LV
J Phys Chem B; 2021 Jan; 125(1):24-35. PubMed ID: 33382616
[TBL] [Abstract][Full Text] [Related]
16. Force Field Benchmark of Amino Acids. 2. Partition Coefficients between Water and Organic Solvents.
Zhang H; Jiang Y; Cui Z; Yin C
J Chem Inf Model; 2018 Aug; 58(8):1669-1681. PubMed ID: 30047730
[TBL] [Abstract][Full Text] [Related]
17. Free energy profile of RNA hairpins: a molecular dynamics simulation study.
Deng NJ; Cieplak P
Biophys J; 2010 Feb; 98(4):627-36. PubMed ID: 20159159
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Modeling the mechanism of CLN025 beta-hairpin formation.
McKiernan KA; Husic BE; Pande VS
J Chem Phys; 2017 Sep; 147(10):104107. PubMed ID: 28915754
[TBL] [Abstract][Full Text] [Related]
20. 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]
[Next] [New Search]
