These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

182 related articles for article (PubMed ID: 22845837)

  • 1. 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]  

  • 2. Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from molecular dynamics.
    Meher BR; Kumar MV; Bandyopadhyay P
    J Biomol Struct Dyn; 2014; 32(6):899-915. PubMed ID: 23782135
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. 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]  

  • 5. Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation.
    Trbovic N; Kim B; Friesner RA; Palmer AG
    Proteins; 2008 May; 71(2):684-94. PubMed ID: 17975832
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. Ensemble fits of restrained peptides' conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3.
    Ciarkowski J; Łuczak S; Jagieła D; Sikorska E; Wójcik J; Oleszczuk M; Izdebski J
    J Mol Graph Model; 2012 Feb; 32():67-74. PubMed ID: 22079210
    [TBL] [Abstract][Full Text] [Related]  

  • 8. [Generalized ordering parameter S2 for N-H peptide bonding as measure of the conformational flexibility of proteins: comparison of algorithms of S2 calculation from molecular dynamics simulation data].
    Koval'skiĭ DB; Ivanova OS; Dubina VN; Kanibolotskiĭ DS; Korneliuk AI
    Ukr Biokhim Zh (1999); 2004; 76(2):128-32. PubMed ID: 15915725
    [TBL] [Abstract][Full Text] [Related]  

  • 9. 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]  

  • 10. 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]  

  • 11. 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]  

  • 12. 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]  

  • 13. Assessing the Current State of Amber Force Field Modifications for DNA.
    Galindo-Murillo R; Robertson JC; Zgarbová M; Šponer J; Otyepka M; Jurečka P; Cheatham TE
    J Chem Theory Comput; 2016 Aug; 12(8):4114-27. PubMed ID: 27300587
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations.
    Duan LL; Zhu T; Li YC; Zhang QG; Zhang JZ
    Sci Rep; 2017 Feb; 7():42223. PubMed ID: 28155907
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.
    Shao Q; Shi J; Zhu W
    J Chem Phys; 2012 Sep; 137(12):125103. PubMed ID: 23020351
    [TBL] [Abstract][Full Text] [Related]  

  • 16. 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]  

  • 17. Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights.
    Chetty S; Bhakat S; Martin AJ; Soliman ME
    J Biomol Struct Dyn; 2016; 34(1):135-51. PubMed ID: 25671669
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.
    Verbaro D; Ghosh I; Nau WM; Schweitzer-Stenner R
    J Phys Chem B; 2010 Dec; 114(51):17201-8. PubMed ID: 21138254
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing.
    Sadiq SK; De Fabritiis G
    Proteins; 2010 Nov; 78(14):2873-85. PubMed ID: 20715057
    [TBL] [Abstract][Full Text] [Related]  

  • 20. On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.
    O'Brien ES; Wand AJ; Sharp KA
    Protein Sci; 2016 Jun; 25(6):1156-60. PubMed ID: 26990788
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.