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 *

220 related articles for article (PubMed ID: 29678106)

  • 1. Uncertainty Quantification in Alchemical Free Energy Methods.
    Bhati AP; Wan S; Hu Y; Sherborne B; Coveney PV
    J Chem Theory Comput; 2018 Jun; 14(6):2867-2880. PubMed ID: 29678106
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols.
    Bhati AP; Coveney PV
    J Chem Theory Comput; 2022 Apr; 18(4):2687-2702. PubMed ID: 35293737
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner's Guide.
    Aldeghi M; Bluck JP; Biggin PC
    Methods Mol Biol; 2018; 1762():199-232. PubMed ID: 29594774
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. Enhanced ligand sampling for relative protein-ligand binding free energy calculations.
    Kaus JW; McCammon JA
    J Phys Chem B; 2015 May; 119(20):6190-7. PubMed ID: 25906170
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility.
    Wade AD; Bhati AP; Wan S; Coveney PV
    J Chem Theory Comput; 2022 Jun; 18(6):3972-3987. PubMed ID: 35609233
    [TBL] [Abstract][Full Text] [Related]  

  • 8. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation.
    Sun ZX; Wang XH; Zhang JZH
    Phys Chem Chem Phys; 2017 Jun; 19(23):15005-15020. PubMed ID: 28555225
    [TBL] [Abstract][Full Text] [Related]  

  • 9. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.
    Rizzi A; Jensen T; Slochower DR; Aldeghi M; Gapsys V; Ntekoumes D; Bosisio S; Papadourakis M; Henriksen NM; de Groot BL; Cournia Z; Dickson A; Michel J; Gilson MK; Shirts MR; Mobley DL; Chodera JD
    J Comput Aided Mol Des; 2020 May; 34(5):601-633. PubMed ID: 31984465
    [TBL] [Abstract][Full Text] [Related]  

  • 10. 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]  

  • 11. Elucidation of Nonadditive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study.
    Calabrò G; Woods CJ; Powlesland F; Mey AS; Mulholland AJ; Michel J
    J Phys Chem B; 2016 Jun; 120(24):5340-50. PubMed ID: 27248478
    [TBL] [Abstract][Full Text] [Related]  

  • 12. CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.
    Zhang H; Kim S; Giese TJ; Lee TS; Lee J; York DM; Im W
    J Chem Inf Model; 2021 Sep; 61(9):4145-4151. PubMed ID: 34521199
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods.
    Hayes RL; Vilseck JZ; Brooks CL
    J Chem Theory Comput; 2022 Apr; 18(4):2114-2123. PubMed ID: 35255214
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Understanding Aldose Reductase-Inhibitors interactions with free energy simulation.
    Sun Z; Wang X; Zhao Q; Zhu T
    J Mol Graph Model; 2019 Sep; 91():10-21. PubMed ID: 31128525
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.
    Lee TS; Allen BK; Giese TJ; Guo Z; Li P; Lin C; McGee TD; Pearlman DA; Radak BK; Tao Y; Tsai HC; Xu H; Sherman W; York DM
    J Chem Inf Model; 2020 Nov; 60(11):5595-5623. PubMed ID: 32936637
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.
    Harger M; Li D; Wang Z; Dalby K; Lagardère L; Piquemal JP; Ponder J; Ren P
    J Comput Chem; 2017 Sep; 38(23):2047-2055. PubMed ID: 28600826
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding.
    Cabeza de Vaca I; Qian Y; Vilseck JZ; Tirado-Rives J; Jorgensen WL
    J Chem Theory Comput; 2018 Jun; 14(6):3279-3288. PubMed ID: 29708338
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series.
    Sabanés Zariquiey F; Pérez A; Majewski M; Gallicchio E; De Fabritiis G
    J Chem Inf Model; 2023 Apr; 63(8):2438-2444. PubMed ID: 37042797
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Classical and Machine Learning Methods for Protein - Ligand Binding Free Energy Estimation.
    Sivakumar D; Wu S
    Curr Drug Metab; 2022; 23(4):252-259. PubMed ID: 35293293
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.