BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

124 related articles for article (PubMed ID: 38717640)

  • 1. Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules.
    Chakravorty A; Hussain A; Cervantes LF; Lai TT; Brooks CL
    J Chem Inf Model; 2024 May; 64(10):4089-4101. PubMed ID: 38717640
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields.
    Fan S; Iorga BI; Beckstein O
    J Comput Aided Mol Des; 2020 May; 34(5):543-560. PubMed ID: 31960254
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Validation of the Generalized Force Fields GAFF, CGenFF, OPLS-AA, and PRODRGFF by Testing Against Experimental Osmotic Coefficient Data for Small Drug-Like Molecules.
    Zhu S
    J Chem Inf Model; 2019 Oct; 59(10):4239-4247. PubMed ID: 31557024
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations.
    Lundborg M; Lindahl E
    J Phys Chem B; 2015 Jan; 119(3):810-23. PubMed ID: 25343332
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Optimized Lennard-Jones Parameters for Druglike Small Molecules.
    Boulanger E; Huang L; Rupakheti C; MacKerell AD; Roux B
    J Chem Theory Comput; 2018 Jun; 14(6):3121-3131. PubMed ID: 29694035
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules.
    Fan S; Nedev H; Vijayan R; Iorga BI; Beckstein O
    J Comput Aided Mol Des; 2021 Jul; 35(7):853-870. PubMed ID: 34232435
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Hydration Free Energies of Multifunctional Nitroaromatic Compounds.
    Ahmed A; Sandler SI
    J Chem Theory Comput; 2013 Jun; 9(6):2774-85. PubMed ID: 26583868
    [TBL] [Abstract][Full Text] [Related]  

  • 8. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
    Vanommeslaeghe K; Hatcher E; Acharya C; Kundu S; Zhong S; Shim J; Darian E; Guvench O; Lopes P; Vorobyov I; Mackerell AD
    J Comput Chem; 2010 Mar; 31(4):671-90. PubMed ID: 19575467
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.
    Shivakumar D; Williams J; Wu Y; Damm W; Shelley J; Sherman W
    J Chem Theory Comput; 2010 May; 6(5):1509-19. PubMed ID: 26615687
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules.
    Vassetti D; Pagliai M; Procacci P
    J Chem Theory Comput; 2019 Mar; 15(3):1983-1995. PubMed ID: 30694667
    [TBL] [Abstract][Full Text] [Related]  

  • 11. FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules.
    Kumar A; Yoluk O; MacKerell AD
    J Comput Chem; 2020 Apr; 41(9):958-970. PubMed ID: 31886576
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free energies.
    Kashefolgheta S; Wang S; Acree WE; Hünenberger PH
    Phys Chem Chem Phys; 2021 Jun; 23(23):13055-13074. PubMed ID: 34105547
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field.
    Karwounopoulos J; Kaupang Å; Wieder M; Boresch S
    J Chem Theory Comput; 2023 Sep; 19(17):5988-5998. PubMed ID: 37616333
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Polarizable Force Field with a σ-Hole for Liquid and Aqueous Bromomethane.
    Adluri AN; Murphy JN; Tozer T; Rowley CN
    J Phys Chem B; 2015 Oct; 119(42):13422-32. PubMed ID: 26419599
    [TBL] [Abstract][Full Text] [Related]  

  • 15. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.
    Kim S; Lee J; Jo S; Brooks CL; Lee HS; Im W
    J Comput Chem; 2017 Jun; 38(21):1879-1886. PubMed ID: 28497616
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.
    Shivakumar D; Deng Y; Roux B
    J Chem Theory Comput; 2009 Apr; 5(4):919-30. PubMed ID: 26609601
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Benchmarking Force Field and the ANI Neural Network Potentials for the Torsional Potential Energy Surface of Biaryl Drug Fragments.
    Lahey SJ; Thien Phuc TN; Rowley CN
    J Chem Inf Model; 2020 Dec; 60(12):6258-6268. PubMed ID: 33263401
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.
    Caleman C; van Maaren PJ; Hong M; Hub JS; Costa LT; van der Spoel D
    J Chem Theory Comput; 2012 Jan; 8(1):61-74. PubMed ID: 22241968
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields.
    Kamath G; Kurnikov I; Fain B; Leontyev I; Illarionov A; Butin O; Olevanov M; Pereyaslavets L
    J Comput Aided Mol Des; 2016 Nov; 30(11):977-988. PubMed ID: 27585472
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Surveying implicit solvent models for estimating small molecule absolute hydration free energies.
    Knight JL; Brooks CL
    J Comput Chem; 2011 Oct; 32(13):2909-23. PubMed ID: 21735452
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.