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 *

169 related articles for article (PubMed ID: 19405629)

  • 1. Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations.
    Ytreberg FM
    J Chem Phys; 2009 Apr; 130(16):164906. PubMed ID: 19405629
    [TBL] [Abstract][Full Text] [Related]  

  • 2. The free energy landscape of small molecule unbinding.
    Huang D; Caflisch A
    PLoS Comput Biol; 2011 Feb; 7(2):e1002002. PubMed ID: 21390201
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Protein Structural Memory Influences Ligand Binding Mode(s) and Unbinding Rates.
    Xu M; Caflisch A; Hamm P
    J Chem Theory Comput; 2016 Mar; 12(3):1393-9. PubMed ID: 26799675
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications.
    Reif MM; Zacharias M
    J Chem Theory Comput; 2022 Jun; 18(6):3873-3893. PubMed ID: 35653503
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Ligand Release Pathways Obtained with WExplore: Residence Times and Mechanisms.
    Dickson A; Lotz SD
    J Phys Chem B; 2016 Jun; 120(24):5377-85. PubMed ID: 27231969
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP.
    Zacharias M
    Proteins; 2004 Mar; 54(4):759-67. PubMed ID: 14997571
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Small molecule binding to proteins: affinity and binding/unbinding dynamics from atomistic simulations.
    Huang D; Caflisch A
    ChemMedChem; 2011 Sep; 6(9):1578-80. PubMed ID: 21674810
    [No Abstract]   [Full Text] [Related]  

  • 8. SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.
    Huai Z; Yang H; Li X; Sun Z
    J Comput Aided Mol Des; 2021 Jan; 35(1):117-129. PubMed ID: 33037549
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations.
    Pan AC; Xu H; Palpant T; Shaw DE
    J Chem Theory Comput; 2017 Jul; 13(7):3372-3377. PubMed ID: 28582625
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations.
    Okimoto N; Suenaga A; Taiji M
    J Biomol Struct Dyn; 2017 Nov; 35(15):3221-3231. PubMed ID: 27771988
    [TBL] [Abstract][Full Text] [Related]  

  • 11. X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies.
    Burkhard P; Taylor P; Walkinshaw MD
    J Mol Biol; 2000 Jan; 295(4):953-62. PubMed ID: 10656803
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Estimation of relative binding free energy based on a free energy variational principle for the FKBP-ligand system.
    Ashida T; Kikuchi T
    J Comput Aided Mol Des; 2013 Jun; 27(6):479-90. PubMed ID: 23754464
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework.
    Giovannelli E; Procacci P; Cardini G; Pagliai M; Volkov V; Chelli R
    J Chem Theory Comput; 2017 Dec; 13(12):5874-5886. PubMed ID: 28992706
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Direct calculation of the binding free energies of FKBP ligands.
    Fujitani H; Tanida Y; Ito M; Jayachandran G; Snow CD; Shirts MR; Sorin EJ; Pande VS
    J Chem Phys; 2005 Aug; 123(8):084108. PubMed ID: 16164283
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Calculation of absolute protein-ligand binding affinity using path and endpoint approaches.
    Lee MS; Olson MA
    Biophys J; 2006 Feb; 90(3):864-77. PubMed ID: 16284269
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations.
    Wolf S; Amaral M; Lowinski M; Vallée F; Musil D; Güldenhaupt J; Dreyer MK; Bomke J; Frech M; Schlitter J; Gerwert K
    J Chem Inf Model; 2019 Dec; 59(12):5135-5147. PubMed ID: 31697501
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation.
    Giovannelli E; Cioni M; Procacci P; Cardini G; Pagliai M; Volkov V; Chelli R
    J Chem Theory Comput; 2017 Dec; 13(12):5887-5899. PubMed ID: 29112430
    [TBL] [Abstract][Full Text] [Related]  

  • 18. II. Dissociation free energies in drug-receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands.
    Nerattini F; Chelli R; Procacci P
    Phys Chem Chem Phys; 2016 Jun; 18(22):15005-18. PubMed ID: 27193181
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity.
    Shi D; Bai Q; Zhou S; Liu X; Liu H; Yao X
    Proteins; 2018 Jan; 86(1):43-56. PubMed ID: 29023988
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Force probe molecular dynamics simulations.
    Grubmüller H
    Methods Mol Biol; 2005; 305():493-515. PubMed ID: 15943012
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.