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 *

126 related articles for article (PubMed ID: 30793836)

  • 1. Lessons learned about steered molecular dynamics simulations and free energy calculations.
    Boubeta FM; Contestín García RM; Lorenzo EN; Boechi L; Estrin D; Sued M; Arrar M
    Chem Biol Drug Des; 2019 Jun; 93(6):1129-1138. PubMed ID: 30793836
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Calculating potentials of mean force from steered molecular dynamics simulations.
    Park S; Schulten K
    J Chem Phys; 2004 Apr; 120(13):5946-61. PubMed ID: 15267476
    [TBL] [Abstract][Full Text] [Related]  

  • 3. On the improvement of free-energy calculation from steered molecular dynamics simulations using adaptive stochastic perturbation protocols.
    Perišić O; Lu H
    PLoS One; 2014; 9(9):e101810. PubMed ID: 25232859
    [TBL] [Abstract][Full Text] [Related]  

  • 4. On the accurate estimation of free energies using the jarzynski equality.
    Arrar M; Boubeta FM; Szretter ME; Sued M; Boechi L; Rodriguez D
    J Comput Chem; 2019 Feb; 40(4):688-696. PubMed ID: 30565267
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments.
    Minh DD; McCammon JA
    J Phys Chem B; 2008 May; 112(19):5892-7. PubMed ID: 18088108
    [TBL] [Abstract][Full Text] [Related]  

  • 6. On the relative merits of equilibrium and non-equilibrium simulations for the estimation of free-energy differences.
    Daura X; Affentranger R; Mark AE
    Chemphyschem; 2010 Dec; 11(17):3734-43. PubMed ID: 21080399
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations.
    Chen LY
    Biophys Chem; 2010 Oct; 151(3):178-80. PubMed ID: 20573441
    [TBL] [Abstract][Full Text] [Related]  

  • 8. A modified Jarzynski free-energy estimator to eliminate non-conservative forces and its application in nanoparticle-membrane interactions.
    Hosseini AN; Lund M; Ejtehadi MR
    Phys Chem Chem Phys; 2022 Feb; 24(6):3647-3654. PubMed ID: 35103740
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics.
    Ramírez CL; Martí MA; Roitberg AE
    Methods Enzymol; 2016; 578():123-43. PubMed ID: 27497165
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Comparison of umbrella sampling and steered molecular dynamics methods for computing free energy profiles of aromatic substrates through phospholipid bilayers.
    Noh SY; Notman R
    J Chem Phys; 2020 Jul; 153(3):034115. PubMed ID: 32716163
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements.
    Gore J; Ritort F; Bustamante C
    Proc Natl Acad Sci U S A; 2003 Oct; 100(22):12564-9. PubMed ID: 14528008
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality.
    Kosztin I; Barz B; Janosi L
    J Chem Phys; 2006 Feb; 124(6):64106. PubMed ID: 16483195
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Seeding the multi-dimensional nonequilibrium pulling for Hamiltonian variation: indirect nonequilibrium free energy simulations at QM levels.
    Sun Z; He Q
    Phys Chem Chem Phys; 2022 Apr; 24(15):8800-8819. PubMed ID: 35352744
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations.
    Okimoto N; Suenaga A; Taiji M
    J Biomol Struct Dyn; 2017 Nov; 35(15):3221-3231. PubMed ID: 27771988
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Theoretical study of enzymatically catalyzed tautomerization of carbon acids in aqueous solution: quantum calculations and steered molecular dynamics simulations.
    Tolosa S; Hidalgo A; Sansón JA
    J Mol Model; 2016 Feb; 22(2):44. PubMed ID: 26815031
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Overcoming dissipation in the calculation of standard binding free energies by ligand extraction.
    Velez-Vega C; Gilson MK
    J Comput Chem; 2013 Oct; 34(27):2360-71. PubMed ID: 24038118
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Unbinding pathway energy of glyphosate from the EPSPs enzyme binding site characterized by Steered Molecular Dynamics and Potential of Mean Force.
    Ferreira MF; Franca EF; Leite FL
    J Mol Graph Model; 2017 Mar; 72():43-49. PubMed ID: 28033555
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin.
    Zhang Z; Santos AP; Zhou Q; Liang L; Wang Q; Wu T; Franzen S
    Biophys Chem; 2016 Apr; 211():28-38. PubMed ID: 26824426
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Hummer and Szabo-like potential of mean force estimator for bidirectional nonequilibrium pulling experiments/simulations.
    Nicolini P; Procacci P; Chelli R
    J Phys Chem B; 2010 Jul; 114(29):9546-54. PubMed ID: 20597536
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Gaussian Accelerated Molecular Dynamics in NAMD.
    Pang YT; Miao Y; Wang Y; McCammon JA
    J Chem Theory Comput; 2017 Jan; 13(1):9-19. PubMed ID: 28034310
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.