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 *

165 related articles for article (PubMed ID: 36659995)

  • 1. Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking.
    Bekker GJ; Kamiya N
    Biophys Rev; 2022 Dec; 14(6):1349-1358. PubMed ID: 36659995
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations.
    Bekker GJ; Fukuda I; Higo J; Fukunishi Y; Kamiya N
    Sci Rep; 2021 Mar; 11(1):5046. PubMed ID: 33658550
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level.
    Bekker GJ; Kamiya N
    Methods Mol Biol; 2021; 2266():187-202. PubMed ID: 33759128
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking.
    Bekker GJ; Araki M; Oshima K; Okuno Y; Kamiya N
    J Chem Inf Model; 2021 Oct; 61(10):5161-5171. PubMed ID: 34549581
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations.
    Bekker GJ; Fukunishi Y; Higo J; Kamiya N
    ACS Omega; 2024 Jan; 9(3):3412-3422. PubMed ID: 38284074
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations.
    Bekker GJ; Araki M; Oshima K; Okuno Y; Kamiya N
    J Phys Chem B; 2019 Mar; 123(11):2479-2490. PubMed ID: 30808168
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking.
    Bekker GJ; Araki M; Oshima K; Okuno Y; Kamiya N
    J Comput Chem; 2020 Jun; 41(17):1606-1615. PubMed ID: 32267975
    [TBL] [Abstract][Full Text] [Related]  

  • 8. N-Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A*2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Simulations.
    Bekker GJ; Kamiya N
    J Phys Chem B; 2021 Dec; 125(49):13376-13384. PubMed ID: 34856806
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor.
    Bekker GJ; Kamiya N; Araki M; Fukuda I; Okuno Y; Nakamura H
    J Chem Theory Comput; 2017 Jun; 13(6):2389-2399. PubMed ID: 28482660
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02.
    Bekker GJ; Numoto N; Kawasaki M; Hayashi T; Yabuno S; Kozono Y; Shimizu T; Kozono H; Ito N; Oda M; Kamiya N
    Protein Sci; 2023 Oct; 32(10):e4775. PubMed ID: 37661929
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others.
    Kamiya N; Yonezawa Y; Nakamura H; Higo J
    Proteins; 2008 Jan; 70(1):41-53. PubMed ID: 17636570
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein-Ligand Sampling.
    Liu W; Liu Z; Liu H; Westerhoff LM; Zheng Z
    J Chem Inf Model; 2022 Nov; 62(22):5645-5665. PubMed ID: 36282990
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
    Foffi G; Pastore A; Piazza F; Temussi PA
    Phys Biol; 2013 Aug; 10(4):040301. PubMed ID: 23912807
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.
    Higo J; Umezawa K
    Adv Exp Med Biol; 2014; 805():331-51. PubMed ID: 24446368
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes.
    Higo J; Ikebe J; Kamiya N; Nakamura H
    Biophys Rev; 2012 Mar; 4(1):27-44. PubMed ID: 22347892
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water.
    Ikebe J; Umezawa K; Kamiya N; Sugihara T; Yonezawa Y; Takano Y; Nakamura H; Higo J
    J Comput Chem; 2011 May; 32(7):1286-97. PubMed ID: 21425286
    [TBL] [Abstract][Full Text] [Related]  

  • 17. A virtual-system coupled multicanonical molecular dynamics simulation: principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent.
    Higo J; Umezawa K; Nakamura H
    J Chem Phys; 2013 May; 138(18):184106. PubMed ID: 23676028
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation.
    Shimoyama H; Nakamura H; Yonezawa Y
    J Chem Phys; 2011 Jan; 134(2):024109. PubMed ID: 21241082
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Studying the binding interactions of allosteric agonists and antagonists of the CXCR4 receptor.
    Planesas JM; Pérez-Nueno VI; Borrell JI; Teixidó J
    J Mol Graph Model; 2015 Jul; 60():1-14. PubMed ID: 26080355
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein.
    Li H; Li C
    J Comput Chem; 2010 Jul; 31(10):2014-22. PubMed ID: 20166125
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.