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 *

361 related articles for article (PubMed ID: 31396898)

  • 1. Force Fields for Small Molecules.
    Lin FY; MacKerell AD
    Methods Mol Biol; 2019; 2022():21-54. PubMed ID: 31396898
    [TBL] [Abstract][Full Text] [Related]  

  • 2. CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.
    Vanommeslaeghe K; MacKerell AD
    Biochim Biophys Acta; 2015 May; 1850(5):861-871. PubMed ID: 25149274
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.
    Lin FY; Lopes PEM; Harder E; Roux B; MacKerell AD
    J Chem Inf Model; 2018 May; 58(5):993-1004. PubMed ID: 29624370
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields.
    Lin FY; MacKerell AD
    J Chem Inf Model; 2019 Jan; 59(1):215-228. PubMed ID: 30418023
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model.
    Baker CM; Anisimov VM; MacKerell AD
    J Phys Chem B; 2011 Jan; 115(3):580-96. PubMed ID: 21166469
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Pairwise-additive and polarizable atomistic force fields for molecular dynamics simulations of proteins.
    Lemkul JA
    Prog Mol Biol Transl Sci; 2020; 170():1-71. PubMed ID: 32145943
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field.
    Rupakheti CR; MacKerell AD; Roux B
    J Chem Theory Comput; 2021 Nov; 17(11):7085-7095. PubMed ID: 34609863
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.
    Yu Y; Venable RM; Thirman J; Chatterjee P; Kumar A; Pastor RW; Roux B; MacKerell AD; Klauda JB
    J Chem Theory Comput; 2023 May; 19(9):2590-2605. PubMed ID: 37071552
    [TBL] [Abstract][Full Text] [Related]  

  • 9. 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]  

  • 10. Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model.
    Lemkul JA
    Methods Mol Biol; 2021; 2315():219-240. PubMed ID: 34302679
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model.
    Zhu X; MacKerell AD
    J Comput Chem; 2010 Sep; 31(12):2330-41. PubMed ID: 20575015
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.
    Huang J; Lemkul JA; Eastman PK; MacKerell AD
    J Comput Chem; 2018 Aug; 39(21):1682-1689. PubMed ID: 29727037
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator.
    He X; Lopes PE; Mackerell AD
    Biopolymers; 2013 Oct; 99(10):724-38. PubMed ID: 23703219
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Molecular Modeling of Water-in-Salt Electrolytes: A Comprehensive Analysis of Polarization Effects and Force Field Parameters in Molecular Dynamics Simulations.
    Rezaei M; Sakong S; Groß A
    J Chem Theory Comput; 2023 Sep; 19(17):5712-5730. PubMed ID: 37528639
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.
    Kognole AA; Aytenfisu AH; MacKerell AD
    J Phys Chem B; 2022 Sep; 126(35):6642-6653. PubMed ID: 36005290
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.
    Kognole AA; Aytenfisu AH; MacKerell AD
    J Mol Model; 2020 May; 26(6):152. PubMed ID: 32447472
    [TBL] [Abstract][Full Text] [Related]  

  • 17. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.
    Kognole AA; Lee J; Park SJ; Jo S; Chatterjee P; Lemkul JA; Huang J; MacKerell AD; Im W
    J Comput Chem; 2022 Feb; 43(5):359-375. PubMed ID: 34874077
    [TBL] [Abstract][Full Text] [Related]  

  • 18. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.
    Lemkul JA; Huang J; Roux B; MacKerell AD
    Chem Rev; 2016 May; 116(9):4983-5013. PubMed ID: 26815602
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.
    Aleksandrov A; Lin FY; Roux B; MacKerell AD
    J Comput Chem; 2018 Aug; 39(22):1707-1719. PubMed ID: 29737546
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Force Field for Peptides and Proteins based on the Classical Drude Oscillator.
    Lopes PE; Huang J; Shim J; Luo Y; Li H; Roux B; Mackerell AD
    J Chem Theory Comput; 2013 Dec; 9(12):5430-5449. PubMed ID: 24459460
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 19.