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 *

168 related articles for article (PubMed ID: 21843482)

  • 1. Toward a predictive understanding of slow methyl group dynamics in proteins.
    Long D; Li DW; Walter KF; Griesinger C; Brüschweiler R
    Biophys J; 2011 Aug; 101(4):910-5. PubMed ID: 21843482
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. 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]  

  • 4. 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]  

  • 5. 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]  

  • 6. Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers.
    Hoffmann F; Mulder FAA; Schäfer LV
    J Chem Phys; 2020 Feb; 152(8):084102. PubMed ID: 32113361
    [TBL] [Abstract][Full Text] [Related]  

  • 7. How accurately do force fields represent protein side chain ensembles?
    Petrović D; Wang X; Strodel B
    Proteins; 2018 Sep; 86(9):935-944. PubMed ID: 29790608
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data.
    Lange OF; van der Spoel D; de Groot BL
    Biophys J; 2010 Jul; 99(2):647-55. PubMed ID: 20643085
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Probing Methyl Group Dynamics in Proteins by NMR Cross-Correlated Dipolar Relaxation and Molecular Dynamics Simulations.
    Ali AAAI; Hoffmann F; Schäfer LV; Mulder FAA
    J Chem Theory Comput; 2022 Dec; 18(12):7722-7732. PubMed ID: 36326619
    [TBL] [Abstract][Full Text] [Related]  

  • 10. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
    Maier JA; Martinez C; Kasavajhala K; Wickstrom L; Hauser KE; Simmerling C
    J Chem Theory Comput; 2015 Aug; 11(8):3696-713. PubMed ID: 26574453
    [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. Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields.
    Hoffmann F; Mulder FAA; Schäfer LV
    J Phys Chem B; 2018 May; 122(19):5038-5048. PubMed ID: 29695158
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins.
    Li DW; Brüschweiler R
    J Chem Theory Comput; 2011 Jun; 7(6):1773-82. PubMed ID: 26596440
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Structural Ensemble of CD4 Cytoplasmic Tail (402-419) Reveals a Nearly Flat Free-Energy Landscape with Local α-Helical Order in Aqueous Solution.
    Ahalawat N; Arora S; Murarka RK
    J Phys Chem B; 2015 Aug; 119(34):11229-42. PubMed ID: 26132982
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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]  

  • 16. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data.
    Huang J; MacKerell AD
    J Comput Chem; 2013 Sep; 34(25):2135-45. PubMed ID: 23832629
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation.
    Xiang X; Hansen AL; Yu L; Jameson G; Bruschweiler-Li L; Yuan C; Brüschweiler R
    J Am Chem Soc; 2021 Sep; 143(34):13593-13604. PubMed ID: 34428032
    [TBL] [Abstract][Full Text] [Related]  

  • 18. 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]  

  • 19. Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.
    Li S; Andrews CT; Frembgen-Kesner T; Miller MS; Siemonsma SL; Collingsworth TD; Rockafellow IT; Ngo NA; Campbell BA; Brown RF; Guo C; Schrodt M; Liu YT; Elcock AH
    J Chem Theory Comput; 2015 Mar; 11(3):1315-29. PubMed ID: 26579777
    [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 9.