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 *

210 related articles for article (PubMed ID: 23197420)

  • 1. (Ala)(4)-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters.
    Shim J; Zhu X; Best RB; MacKerell AD
    J Comput Chem; 2013 Mar; 34(7):593-603. PubMed ID: 23197420
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.
    Lin FY; Huang J; Pandey P; Rupakheti C; Li J; Roux BT; MacKerell AD
    J Chem Theory Comput; 2020 May; 16(5):3221-3239. PubMed ID: 32282198
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation.
    Feng Y; Huang J; Kim S; Shim JH; MacKerell AD; Ge NH
    J Phys Chem B; 2016 Jun; 120(24):5325-39. PubMed ID: 27299801
    [TBL] [Abstract][Full Text] [Related]  

  • 4. N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent.
    Goyal B; Srivastava KR; Durani S
    J Pept Sci; 2017 Jun; 23(6):431-437. PubMed ID: 28425159
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Influence of side chain conformations on local conformational features of amino acids and implication for force field development.
    Jiang F; Han W; Wu YD
    J Phys Chem B; 2010 May; 114(17):5840-50. PubMed ID: 20392111
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. 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]  

  • 8. Intrinsic α-helical and β-sheet conformational preferences: a computational case study of alanine.
    Caballero D; Määttä J; Zhou AQ; Sammalkorpi M; O'Hern CS; Regan L
    Protein Sci; 2014 Jul; 23(7):970-80. PubMed ID: 24753338
    [TBL] [Abstract][Full Text] [Related]  

  • 9. The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development.
    Jiang F; Han W; Wu YD
    Phys Chem Chem Phys; 2013 Mar; 15(10):3413-28. PubMed ID: 23385383
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
    Mackerell AD; Feig M; Brooks CL
    J Comput Chem; 2004 Aug; 25(11):1400-15. PubMed ID: 15185334
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Fine grained sampling of residue characteristics using molecular dynamics simulation.
    Joo H; Qu X; Swanson R; McCallum CM; Tsai J
    Comput Biol Chem; 2010 Jun; 34(3):172-83. PubMed ID: 20621565
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Intrinsic energy landscapes of amino acid side-chains.
    Zhu X; Lopes PE; Shim J; MacKerell AD
    J Chem Inf Model; 2012 Jun; 52(6):1559-72. PubMed ID: 22582825
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.
    Best RB; Zhu X; Shim J; Lopes PE; Mittal J; Feig M; Mackerell AD
    J Chem Theory Comput; 2012 Sep; 8(9):3257-3273. PubMed ID: 23341755
    [TBL] [Abstract][Full Text] [Related]  

  • 14. 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]  

  • 15. Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides.
    Wang ZX; Zhang W; Wu C; Lei H; Cieplak P; Duan Y
    J Comput Chem; 2006 Apr; 27(6):781-90. PubMed ID: 16526038
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.
    Liu Y; Beveridge DL
    Proteins; 2002 Jan; 46(1):128-46. PubMed ID: 11746709
    [TBL] [Abstract][Full Text] [Related]  

  • 17. A backbone-dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations.
    Mortensen JC; Damjanovic J; Miao J; Hui T; Lin YS
    Protein Sci; 2022 Dec; 31(12):e4491. PubMed ID: 36327064
    [TBL] [Abstract][Full Text] [Related]  

  • 18. The utility of side-chain cyclization in determining the receptor-bound conformation of peptides: cyclic tripeptides and angiotensin II.
    Kataoka T; Beusen DD; Clark JD; Yodo M; Marshall GR
    Biopolymers; 1992 Nov; 32(11):1519-33. PubMed ID: 1333831
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.
    Hu H; Elstner M; Hermans J
    Proteins; 2003 Feb; 50(3):451-63. PubMed ID: 12557187
    [TBL] [Abstract][Full Text] [Related]  

  • 20. A Maximum-Likelihood Approach to Force-Field Calibration.
    Zaborowski B; Jagieła D; Czaplewski C; Hałabis A; Lewandowska A; Żmudzińska W; Ołdziej S; Karczyńska A; Omieczynski C; Wirecki T; Liwo A
    J Chem Inf Model; 2015 Sep; 55(9):2050-70. PubMed ID: 26263302
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.