BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

227 related articles for article (PubMed ID: 26575575)

  • 1. pKa values in proteins determined by electrostatics applied to molecular dynamics trajectories.
    Meyer T; Knapp EW
    J Chem Theory Comput; 2015 Jun; 11(6):2827-40. PubMed ID: 26575575
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Electrostatic pKa computations in proteins: role of internal cavities.
    Meyer T; Kieseritzky G; Knapp EW
    Proteins; 2011 Dec; 79(12):3320-32. PubMed ID: 21744394
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Effect of a buried ion pair in the hydrophobic core of a protein: An insight from constant pH molecular dynamics study.
    Pathak AK
    Biopolymers; 2015 Mar; 103(3):148-57. PubMed ID: 25363335
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Multiple protonation equilibria in electrostatics of protein-protein binding.
    Piłat Z; Antosiewicz JM
    J Phys Chem B; 2008 Nov; 112(47):15074-85. PubMed ID: 18950218
    [TBL] [Abstract][Full Text] [Related]  

  • 5. 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]  

  • 6. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.
    Li X; Hassan SA; Mehler EL
    Proteins; 2005 Aug; 60(3):464-84. PubMed ID: 15959866
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Optimizing pKa computation in proteins with pH adapted conformations.
    Kieseritzky G; Knapp EW
    Proteins; 2008 May; 71(3):1335-48. PubMed ID: 18058906
    [TBL] [Abstract][Full Text] [Related]  

  • 8. 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]  

  • 9. GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: p
    Harris RC; Shen J
    J Chem Inf Model; 2019 Nov; 59(11):4821-4832. PubMed ID: 31661616
    [TBL] [Abstract][Full Text] [Related]  

  • 10. p
    Aleksandrov A; Roux B; MacKerell AD
    J Chem Theory Comput; 2020 Jul; 16(7):4655-4668. PubMed ID: 32464053
    [TBL] [Abstract][Full Text] [Related]  

  • 11. pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa.
    Wang L; Li L; Alexov E
    Proteins; 2015 Dec; 83(12):2186-97. PubMed ID: 26408449
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Monte Carlo simulations of proteins at constant pH with generalized Born solvent, flexible sidechains, and an effective dielectric boundary.
    Polydorides S; Simonson T
    J Comput Chem; 2013 Dec; 34(31):2742-56. PubMed ID: 24122878
    [TBL] [Abstract][Full Text] [Related]  

  • 13. pK(A) in proteins solving the Poisson-Boltzmann equation with finite elements.
    Sakalli I; Knapp EW
    J Comput Chem; 2015 Nov; 36(29):2147-57. PubMed ID: 26284944
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Extensive Assessment of Various Computational Methods for Aspartate's pK
    Sun Z; Wang X; Song J
    J Chem Inf Model; 2017 Jul; 57(7):1621-1639. PubMed ID: 28644624
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Orthogonal Electric Field Measurements near the Green Fluorescent Protein Fluorophore through Stark Effect Spectroscopy and pK
    Slocum JD; First JT; Webb LJ
    J Phys Chem B; 2017 Jul; 121(28):6799-6812. PubMed ID: 28650636
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Electrostatic contributions to the stability of halophilic proteins.
    Elcock AH; McCammon JA
    J Mol Biol; 1998 Jul; 280(4):731-48. PubMed ID: 9677300
    [TBL] [Abstract][Full Text] [Related]  

  • 17. A detailed representation of electrostatic energy in prediction of sequence and pH dependence of protein stability.
    Dudek MJ
    Proteins; 2014 Oct; 82(10):2497-511. PubMed ID: 24863377
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins.
    Vorobjev YN; Scheraga HA; Vila JA
    J Biomol Struct Dyn; 2018 Feb; 36(3):561-574. PubMed ID: 28132613
    [TBL] [Abstract][Full Text] [Related]  

  • 19. GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber.
    Harris JA; Liu R; Martins de Oliveira V; Vázquez-Montelongo EA; Henderson JA; Shen J
    J Chem Theory Comput; 2022 Dec; 18(12):7510-7527. PubMed ID: 36377980
    [TBL] [Abstract][Full Text] [Related]  

  • 20. 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]  

    [Next]    [New Search]
    of 12.