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 *

180 related articles for article (PubMed ID: 33886305)

  • 1. Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations.
    Nelson L; Bariami S; Ringrose C; Horton JT; Kurdekar V; Mey ASJS; Michel J; Cole DJ
    J Chem Inf Model; 2021 May; 61(5):2124-2130. PubMed ID: 33886305
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages.
    Loeffler HH; Bosisio S; Duarte Ramos Matos G; Suh D; Roux B; Mobley DL; Michel J
    J Chem Theory Comput; 2018 Nov; 14(11):5567-5582. PubMed ID: 30289712
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. 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]  

  • 5. A Python tool to set up relative free energy calculations in GROMACS.
    Klimovich PV; Mobley DL
    J Comput Aided Mol Des; 2015 Nov; 29(11):1007-14. PubMed ID: 26487189
    [TBL] [Abstract][Full Text] [Related]  

  • 6. BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations.
    Fu H; Chen H; Cai W; Shao X; Chipot C
    J Chem Inf Model; 2021 May; 61(5):2116-2123. PubMed ID: 33906354
    [TBL] [Abstract][Full Text] [Related]  

  • 7. 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]  

  • 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. Alchemical prediction of hydration free energies for SAMPL.
    Mobley DL; Liu S; Cerutti DS; Swope WC; Rice JE
    J Comput Aided Mol Des; 2012 May; 26(5):551-62. PubMed ID: 22198475
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Alchemical Free Energy Calculations on Membrane-Associated Proteins.
    Papadourakis M; Sinenka H; Matricon P; Hénin J; Brannigan G; Pérez-Benito L; Pande V; van Vlijmen H; de Graaf C; Deflorian F; Tresadern G; Cecchini M; Cournia Z
    J Chem Theory Comput; 2023 Nov; 19(21):7437-7458. PubMed ID: 37902715
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method.
    Azimi S; Khuttan S; Wu JZ; Pal RK; Gallicchio E
    J Chem Inf Model; 2022 Jan; 62(2):309-323. PubMed ID: 34990555
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software.
    Khalak Y; Tresadern G; de Groot BL; Gapsys V
    J Comput Aided Mol Des; 2021 Jan; 35(1):49-61. PubMed ID: 33230742
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. 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]  

  • 15. 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]  

  • 16. Combining Alchemical Transformation with a Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites.
    Cruz J; Wickstrom L; Yang D; Gallicchio E; Deng N
    J Chem Theory Comput; 2020 Apr; 16(4):2803-2813. PubMed ID: 32101691
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands.
    Chen L; Wu Y; Wu C; Silveira A; Sherman W; Xu H; Gallicchio E
    J Chem Inf Model; 2024 Jan; 64(1):250-264. PubMed ID: 38147877
    [TBL] [Abstract][Full Text] [Related]  

  • 18. 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]  

  • 19. 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]  

  • 20. Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program.
    Wieder M; Fleck M; Braunsfeld B; Boresch S
    J Comput Chem; 2022 Jun; 43(17):1151-1160. PubMed ID: 35485139
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.