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 *

129 related articles for article (PubMed ID: 38323915)

  • 1. Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations.
    Karrenbrock M; Rizzi V; Procacci P; Gervasio FL
    J Phys Chem B; 2024 Feb; 128(7):1595-1605. PubMed ID: 38323915
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.
    Huai Z; Yang H; Li X; Sun Z
    J Comput Aided Mol Des; 2021 Jan; 35(1):117-129. PubMed ID: 33037549
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. Alchemical determination of drug-receptor binding free energy: Where we stand and where we could move to.
    Procacci P
    J Mol Graph Model; 2017 Jan; 71():233-241. PubMed ID: 27984798
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. Calculations of Absolute Free Energies, Enthalpies, and Entropies for Drug Binding.
    Summa CM; Langford DP; Dinshaw SH; Webb J; Rick SW
    J Chem Theory Comput; 2024 Apr; 20(7):2812-2819. PubMed ID: 38538531
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4.
    Guest EE; Cervantes LF; Pickett SD; Brooks CL; Hirst JD
    J Chem Inf Model; 2022 Mar; 62(6):1458-1470. PubMed ID: 35258972
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation.
    Giovannelli E; Cioni M; Procacci P; Cardini G; Pagliai M; Volkov V; Chelli R
    J Chem Theory Comput; 2017 Dec; 13(12):5887-5899. PubMed ID: 29112430
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain.
    Heinzelmann G; Henriksen NM; Gilson MK
    J Chem Theory Comput; 2017 Jul; 13(7):3260-3275. PubMed ID: 28564537
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations.
    Baumann HM; Gapsys V; de Groot BL; Mobley DL
    J Phys Chem B; 2021 May; 125(17):4241-4261. PubMed ID: 33905257
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Comparing the Performance of Different AMBER Protein Forcefields, Partial Charge Assignments, and Water Models for Absolute Binding Free Energy Calculations.
    Huggins DJ
    J Chem Theory Comput; 2022 Apr; 18(4):2616-2630. PubMed ID: 35266690
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.
    Zhang I; Rufa DA; Pulido I; Henry MM; Rosen LE; Hauser K; Singh S; Chodera JD
    J Chem Theory Comput; 2023 Aug; 19(15):4863-4882. PubMed ID: 37450482
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations?
    Procacci P
    Molecules; 2022 Jul; 27(14):. PubMed ID: 35889299
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations.
    Clark F; Robb G; Cole DJ; Michel J
    J Chem Theory Comput; 2023 Jun; 19(12):3686-3704. PubMed ID: 37285579
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Perspective: Alchemical free energy calculations for drug discovery.
    Mobley DL; Klimovich PV
    J Chem Phys; 2012 Dec; 137(23):230901. PubMed ID: 23267463
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework.
    Giovannelli E; Procacci P; Cardini G; Pagliai M; Volkov V; Chelli R
    J Chem Theory Comput; 2017 Dec; 13(12):5874-5886. PubMed ID: 28992706
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics.
    Procacci P
    Curr Opin Struct Biol; 2021 Apr; 67():127-134. PubMed ID: 33220532
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease.
    Macchiagodena M; Pagliai M; Karrenbrock M; Guarnieri G; Iannone F; Procacci P
    J Chem Theory Comput; 2020 Nov; 16(11):7160-7172. PubMed ID: 33090785
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.