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 *

130 related articles for article (PubMed ID: 32770896)

  • 1. Hybrid MC/MD for protein design.
    Michael E; Polydorides S; Simonson T; Archontis G
    J Chem Phys; 2020 Aug; 153(5):054113. PubMed ID: 32770896
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. A Hybrid Monte Carlo Scheme for Multibackbone Protein Design.
    Druart K; Bigot J; Audit E; Simonson T
    J Chem Theory Comput; 2016 Dec; 12(12):6035-6048. PubMed ID: 27775883
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Protein p K
    Villa F; Simonson T
    J Chem Theory Comput; 2018 Dec; 14(12):6714-6721. PubMed ID: 30431264
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.
    Radak BK; Chipot C; Suh D; Jo S; Jiang W; Phillips JC; Schulten K; Roux B
    J Chem Theory Comput; 2017 Dec; 13(12):5933-5944. PubMed ID: 29111720
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. 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]  

  • 8. Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solvent.
    Aleksandrov A; Polydorides S; Archontis G; Simonson T
    J Phys Chem B; 2010 Aug; 114(32):10634-48. PubMed ID: 20701391
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Physics-Based Computational Protein Design: An Update.
    Mignon D; Druart K; Michael E; Opuu V; Polydorides S; Villa F; Gaillard T; Panel N; Archontis G; Simonson T
    J Phys Chem A; 2020 Dec; 124(51):10637-10648. PubMed ID: 33170681
    [TBL] [Abstract][Full Text] [Related]  

  • 10. A simple model of backbone flexibility improves modeling of side-chain conformational variability.
    Friedland GD; Linares AJ; Smith CA; Kortemme T
    J Mol Biol; 2008 Jul; 380(4):757-74. PubMed ID: 18547586
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.
    Yang K; Różycki B; Cui F; Shi C; Chen W; Li Y
    PLoS One; 2016; 11(5):e0156043. PubMed ID: 27227775
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method.
    Chen Y; Roux B
    J Chem Theory Comput; 2015 Aug; 11(8):3919-31. PubMed ID: 26300709
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures.
    Lasham J; Djurabekova A; Zickermann V; Vonck J; Sharma V
    J Phys Chem B; 2024 Mar; 128(10):2304-2316. PubMed ID: 38430110
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Mixed Monte Carlo/Molecular Dynamics simulations of the prion protein.
    Ribeiro AA; de Alencastro RB
    J Mol Graph Model; 2013 May; 42():1-6. PubMed ID: 23501158
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Conformational space exploration of Met- and Leu-enkephalin using the MOLS method, molecular dynamics, and Monte Carlo simulation--a comparative study.
    Ramya L; Gautham N
    Biopolymers; 2012 Mar; 97(3):165-76. PubMed ID: 21953081
    [TBL] [Abstract][Full Text] [Related]  

  • 17. 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]  

  • 18. Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.
    Bürgi R; Kollman PA; Van Gunsteren WF
    Proteins; 2002 Jun; 47(4):469-80. PubMed ID: 12001225
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic.
    Mignon D; Simonson T
    J Comput Chem; 2016 Jul; 37(19):1781-93. PubMed ID: 27197555
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties.
    Alexov EG; Gunner MR
    Biophys J; 1997 May; 72(5):2075-93. PubMed ID: 9129810
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.