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 *

256 related articles for article (PubMed ID: 34302679)

  • 1. 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]  

  • 2. 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]  

  • 3. Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models.
    Davis JE; Rahaman O; Patel S
    Biophys J; 2009 Jan; 96(2):385-402. PubMed ID: 19167291
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.
    Lemkul JA; Roux B; van der Spoel D; MacKerell AD
    J Comput Chem; 2015 Jul; 36(19):1473-9. PubMed ID: 25962472
    [TBL] [Abstract][Full Text] [Related]  

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

  • 7. 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]  

  • 8. Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field.
    Sengul MY; MacKerell AD
    J Comput Biophys Chem; 2022 Jun; 21(4):461-471. PubMed ID: 35756549
    [TBL] [Abstract][Full Text] [Related]  

  • 9. CHARMM-GUI 10 years for biomolecular modeling and simulation.
    Jo S; Cheng X; Lee J; Kim S; Park SJ; Patel DS; Beaven AH; Lee KI; Rui H; Park S; Lee HS; Roux B; MacKerell AD; Klauda JB; Qi Y; Im W
    J Comput Chem; 2017 Jun; 38(15):1114-1124. PubMed ID: 27862047
    [TBL] [Abstract][Full Text] [Related]  

  • 10. 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]  

  • 11. Evaluating Polarizable Biomembrane Simulations against Experiments.
    Antila HS; Dixit S; Kav B; Madsen JJ; Miettinen MS; Ollila OHS
    J Chem Theory Comput; 2024 May; 20(10):4325-4337. PubMed ID: 38718349
    [TBL] [Abstract][Full Text] [Related]  

  • 12. 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]  

  • 13. Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.
    Lin FY; Huang J; Pandey P; Rupakheti C; Li J; Roux BT; MacKerell AD
    J Chem Theory Comput; 2020 May; 16(5):3221-3239. PubMed ID: 32282198
    [TBL] [Abstract][Full Text] [Related]  

  • 14. 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]  

  • 15. 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]  

  • 16. 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]  

  • 17. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model.
    Huang J; Lopes PE; Roux B; MacKerell AD
    J Phys Chem Lett; 2014 Sep; 5(18):3144-3150. PubMed ID: 25247054
    [TBL] [Abstract][Full Text] [Related]  

  • 18. 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]  

  • 19. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.
    Patel S; Mackerell AD; Brooks CL
    J Comput Chem; 2004 Sep; 25(12):1504-14. PubMed ID: 15224394
    [TBL] [Abstract][Full Text] [Related]  

  • 20. DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields.
    Bernardes CES
    J Chem Inf Model; 2022 Mar; 62(6):1471-1478. PubMed ID: 35239343
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 13.