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 *

455 related articles for article (PubMed ID: 15053606)

  • 1. Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
    Simonson T; Carlsson J; Case DA
    J Am Chem Soc; 2004 Apr; 126(13):4167-80. PubMed ID: 15053606
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
    Hassan SA; Mehler EL; Zhang D; Weinstein H
    Proteins; 2003 Apr; 51(1):109-25. PubMed ID: 12596268
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.
    Olson MA
    Proteins; 2004 Dec; 57(4):645-50. PubMed ID: 15481087
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
    Riccardi D; Schaefer P; Cui Q
    J Phys Chem B; 2005 Sep; 109(37):17715-33. PubMed ID: 16853267
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Proton binding to proteins: a free-energy component analysis using a dielectric continuum model.
    Archontis G; Simonson T
    Biophys J; 2005 Jun; 88(6):3888-904. PubMed ID: 15821163
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory.
    Thomas AS; Elcock AH
    J Am Chem Soc; 2006 Jun; 128(24):7796-806. PubMed ID: 16771493
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment.
    Chocholousová J; Feig M
    J Phys Chem B; 2006 Aug; 110(34):17240-51. PubMed ID: 16928023
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Calculations of electrostatic interactions and pKas in the active site of Escherichia coli thioredoxin.
    Dillet V; Dyson HJ; Bashford D
    Biochemistry; 1998 Jul; 37(28):10298-306. PubMed ID: 9665738
    [TBL] [Abstract][Full Text] [Related]  

  • 10. A semi-implicit solvent model for the simulation of peptides and proteins.
    Basdevant N; Borgis D; Ha-Duong T
    J Comput Chem; 2004 Jun; 25(8):1015-29. PubMed ID: 15067677
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
    Morreale A; de la Cruz X; Meyer T; Gelpí JL; Luque FJ; Orozco M
    Proteins; 2004 Nov; 57(3):458-67. PubMed ID: 15382247
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations.
    Kuhn B; Kollman PA; Stahl M
    J Comput Chem; 2004 Nov; 25(15):1865-72. PubMed ID: 15376253
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method.
    Lee MS; Olson MA
    J Phys Chem B; 2005 Mar; 109(11):5223-36. PubMed ID: 16863188
    [TBL] [Abstract][Full Text] [Related]  

  • 14. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.
    Patel S; Mackerell AD; Brooks CL
    J Comput Chem; 2004 Sep; 25(12):1504-14. PubMed ID: 15224394
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics.
    Wang J; Tan C; Chanco E; Luo R
    Phys Chem Chem Phys; 2010 Feb; 12(5):1194-202. PubMed ID: 20094685
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Toward the accurate first-principles prediction of ionization equilibria in proteins.
    Khandogin J; Brooks CL
    Biochemistry; 2006 Aug; 45(31):9363-73. PubMed ID: 16878971
    [TBL] [Abstract][Full Text] [Related]  

  • 17. FACTS: Fast analytical continuum treatment of solvation.
    Haberthür U; Caflisch A
    J Comput Chem; 2008 Apr; 29(5):701-15. PubMed ID: 17918282
    [TBL] [Abstract][Full Text] [Related]  

  • 18. How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis.
    Tan C; Yang L; Luo R
    J Phys Chem B; 2006 Sep; 110(37):18680-7. PubMed ID: 16970499
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.
    Wallace JA; Wang Y; Shi C; Pastoor KJ; Nguyen BL; Xia K; Shen JK
    Proteins; 2011 Dec; 79(12):3364-73. PubMed ID: 21748801
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins.
    Schwarzl SM; Huang D; Smith JC; Fischer S
    J Comput Chem; 2005 Oct; 26(13):1359-71. PubMed ID: 16021598
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 23.