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235 related items for PubMed ID: 34152264

  • 1. Modeling structural interconversion in Alzheimers' amyloid beta peptide with classical and intrinsically disordered protein force fields.
    Wu KY, Doan D, Medrano M, Chang CA.
    J Biomol Struct Dyn; 2022; 40(20):10005-10022. PubMed ID: 34152264
    [Abstract] [Full Text] [Related]

  • 2. Secondary structures transition of tau protein with intrinsically disordered proteins specific force field.
    Dan A, Chen HF.
    Chem Biol Drug Des; 2019 Mar; 93(3):242-253. PubMed ID: 30259679
    [Abstract] [Full Text] [Related]

  • 3. A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta.
    Smardz P, Anila MM, Rogowski P, Li MS, Różycki B, Krupa P.
    Int J Mol Sci; 2024 Jun 18; 25(12):. PubMed ID: 38928405
    [Abstract] [Full Text] [Related]

  • 4. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.
    Watts CR, Gregory A, Frisbie C, Lovas S.
    Proteins; 2018 Mar 18; 86(3):279-300. PubMed ID: 29235155
    [Abstract] [Full Text] [Related]

  • 5. Characterization of the Conformations of Amyloid Beta 42 in Solution That May Mediate Its Initial Hydrophobic Aggregation.
    Sonar K, Mancera RL.
    J Phys Chem B; 2022 Oct 13; 126(40):7916-7933. PubMed ID: 36179370
    [Abstract] [Full Text] [Related]

  • 6. Impact of K16A and K28A mutation on the structure and dynamics of amyloid-β42 peptide in Alzheimer's disease: key insights from molecular dynamics simulations.
    Shuaib S, Saini RK, Goyal D, Goyal B.
    J Biomol Struct Dyn; 2020 Feb 13; 38(3):708-721. PubMed ID: 30821624
    [Abstract] [Full Text] [Related]

  • 7. The structures of the E22Δ mutant-type amyloid-β alloforms and the impact of E22Δ mutation on the structures of the wild-type amyloid-β alloforms.
    Coskuner O, Wise-Scira O, Perry G, Kitahara T.
    ACS Chem Neurosci; 2013 Feb 20; 4(2):310-20. PubMed ID: 23421682
    [Abstract] [Full Text] [Related]

  • 8. Comparison and Evaluation of Force Fields for Intrinsically Disordered Proteins.
    Rahman MU, Rehman AU, Liu H, Chen HF.
    J Chem Inf Model; 2020 Oct 26; 60(10):4912-4923. PubMed ID: 32816485
    [Abstract] [Full Text] [Related]

  • 9. Exploring Structural Insights of Aβ42 and α-Synuclein Monomers and Heterodimer: A Comparative Study Using Implicit and Explicit Solvent Simulations.
    Varenyk Y, Theodorakis PE, Pham DQH, Li MS, Krupa P.
    J Phys Chem B; 2024 May 16; 128(19):4655-4669. PubMed ID: 38700150
    [Abstract] [Full Text] [Related]

  • 10. Comparison of force fields for Alzheimer's A β42: A case study for intrinsically disordered proteins.
    Carballo-Pacheco M, Strodel B.
    Protein Sci; 2017 Feb 16; 26(2):174-185. PubMed ID: 27727496
    [Abstract] [Full Text] [Related]

  • 11. Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach.
    Rosenman DJ, Connors CR, Chen W, Wang C, García AE.
    J Mol Biol; 2013 Sep 23; 425(18):3338-59. PubMed ID: 23811057
    [Abstract] [Full Text] [Related]

  • 12. An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations.
    Kaur A, Goyal D, Goyal B.
    Phys Chem Chem Phys; 2020 Dec 23; 22(48):28055-28073. PubMed ID: 33289734
    [Abstract] [Full Text] [Related]

  • 13. Structure Comparison of Beta Amyloid Peptide Aβ 1-42 Isoforms. Molecular Dynamics Modeling.
    Tolstova AP, Makarov AA, Adzhubei AA.
    J Chem Inf Model; 2024 Feb 12; 64(3):918-932. PubMed ID: 38241093
    [Abstract] [Full Text] [Related]

  • 14. The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins.
    Song D, Luo R, Chen HF.
    J Chem Inf Model; 2017 May 22; 57(5):1166-1178. PubMed ID: 28448138
    [Abstract] [Full Text] [Related]

  • 15. General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins.
    Shabane PS, Izadi S, Onufriev AV.
    J Chem Theory Comput; 2019 Apr 09; 15(4):2620-2634. PubMed ID: 30865832
    [Abstract] [Full Text] [Related]

  • 16. Molecular dynamics simulations of an α-synuclein NAC domain fragment with a ff14IDPSFF IDP-specific force field suggest β-sheet intermediate states of fibrillation.
    Privat C, Madurga S, Mas F, Rubio-Martinez J.
    Phys Chem Chem Phys; 2022 Aug 10; 24(31):18841-18853. PubMed ID: 35912724
    [Abstract] [Full Text] [Related]

  • 17. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β42 in water.
    Weber OC, Uversky VN.
    Intrinsically Disord Proteins; 2017 Aug 10; 5(1):e1377813. PubMed ID: 30250773
    [Abstract] [Full Text] [Related]

  • 18. Zinc binding promotes greater hydrophobicity in Alzheimer's Aβ42 peptide than copper binding: Molecular dynamics and solvation thermodynamics studies.
    Boopathi S, Dinh Quoc Huy P, Gonzalez W, Theodorakis PE, Li MS.
    Proteins; 2020 Oct 10; 88(10):1285-1302. PubMed ID: 32419254
    [Abstract] [Full Text] [Related]

  • 19. Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Solvation.
    Blinov N, Wishart DS, Kovalenko A.
    J Phys Chem B; 2019 Mar 21; 123(11):2491-2506. PubMed ID: 30811210
    [Abstract] [Full Text] [Related]

  • 20. Molecular dynamics study of conformation transition from helix to sheet of Aβ42 peptide.
    Zhou M, Wen H, Lei H, Zhang T.
    J Mol Graph Model; 2021 Dec 21; 109():108027. PubMed ID: 34534891
    [Abstract] [Full Text] [Related]

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