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 *

185 related articles for article (PubMed ID: 29270990)

  • 1. Using the fast fourier transform in binding free energy calculations.
    Nguyen TH; Zhou HX; Minh DDL
    J Comput Chem; 2018 Apr; 39(11):621-636. PubMed ID: 29270990
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations.
    Xie B; Nguyen TH; Minh DDL
    J Chem Theory Comput; 2017 Jun; 13(6):2930-2944. PubMed ID: 28430432
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.
    Minh DDL
    J Comput Chem; 2020 Mar; 41(7):715-730. PubMed ID: 31397498
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Implicit ligand theory for relative binding free energies.
    Nguyen TH; Minh DDL
    J Chem Phys; 2018 Mar; 148(10):104114. PubMed ID: 29544299
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses.
    Sakae Y; Zhang BW; Levy RM; Deng N
    J Comput Chem; 2020 Jan; 41(1):56-68. PubMed ID: 31621932
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.
    Gill SC; Lim NM; Grinaway PB; Rustenburg AS; Fass J; Ross GA; Chodera JD; Mobley DL
    J Phys Chem B; 2018 May; 122(21):5579-5598. PubMed ID: 29486559
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking.
    Minh DD
    J Chem Phys; 2012 Sep; 137(10):104106. PubMed ID: 22979849
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications.
    Reif MM; Zacharias M
    J Chem Theory Comput; 2022 Jun; 18(6):3873-3893. PubMed ID: 35653503
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.
    Jiang W; Thirman J; Jo S; Roux B
    J Phys Chem B; 2018 Oct; 122(41):9435-9442. PubMed ID: 30253098
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Ligand-receptor affinities computed by an adapted linear interaction model for continuum electrostatics and by protein conformational averaging.
    Nunes-Alves A; Arantes GM
    J Chem Inf Model; 2014 Aug; 54(8):2309-19. PubMed ID: 25076043
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Protein-ligand binding free energies from exhaustive docking.
    Purisima EO; Hogues H
    J Phys Chem B; 2012 Jun; 116(23):6872-9. PubMed ID: 22432509
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 : Binding free energies between flexible ligands and rigid receptors.
    Xie B; Minh DDL
    J Comput Aided Mol Des; 2019 Jan; 33(1):61-69. PubMed ID: 30084078
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package.
    Mermelstein DJ; Lin C; Nelson G; Kretsch R; McCammon JA; Walker RC
    J Comput Chem; 2018 Jul; 39(19):1354-1358. PubMed ID: 29532496
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Improved mapping of protein binding sites.
    Kortvelyesi T; Silberstein M; Dennis S; Vajda S
    J Comput Aided Mol Des; 2003; 17(2-4):173-86. PubMed ID: 13677484
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Grand canonical Monte Carlo simulation of ligand-protein binding.
    Clark M; Guarnieri F; Shkurko I; Wiseman J
    J Chem Inf Model; 2006; 46(1):231-42. PubMed ID: 16426059
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Sensitivity in Binding Free Energies Due to Protein Reorganization.
    Lim NM; Wang L; Abel R; Mobley DL
    J Chem Theory Comput; 2016 Sep; 12(9):4620-31. PubMed ID: 27462935
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Testing a flexible-receptor docking algorithm in a model binding site.
    Wei BQ; Weaver LH; Ferrari AM; Matthews BW; Shoichet BK
    J Mol Biol; 2004 Apr; 337(5):1161-82. PubMed ID: 15046985
    [TBL] [Abstract][Full Text] [Related]  

  • 18. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.
    Kaus JW; Harder E; Lin T; Abel R; McCammon JA; Wang L
    J Chem Theory Comput; 2015 Jun; 11(6):2670-9. PubMed ID: 26085821
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant.
    Macaya L; González D; Vöhringer-Martinez E
    J Chem Inf Model; 2024 Apr; 64(8):3269-3277. PubMed ID: 38546407
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Advances in Docking.
    Sulimov VB; Kutov DC; Sulimov AV
    Curr Med Chem; 2019; 26(42):7555-7580. PubMed ID: 30182836
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.