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 *

358 related articles for article (PubMed ID: 32635537)

  • 21. Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.
    Lee J; Tofoleanu F; Pickard FC; König G; Huang J; Damjanović A; Baek M; Seok C; Brooks BR
    J Comput Aided Mol Des; 2017 Jan; 31(1):71-85. PubMed ID: 27677749
    [TBL] [Abstract][Full Text] [Related]  

  • 22. Design and development of high affinity dual anticancer peptide-inhibitors against p53-MDM2/X interaction.
    Rasafar N; Barzegar A; Mehdizadeh Aghdam E
    Life Sci; 2020 Mar; 245():117358. PubMed ID: 32001262
    [TBL] [Abstract][Full Text] [Related]  

  • 23. Differential binding of p53 and nutlin to MDM2 and MDMX: computational studies.
    Joseph TL; Madhumalar A; Brown CJ; Lane DP; Verma CS
    Cell Cycle; 2010 Mar; 9(6):1167-81. PubMed ID: 20190571
    [TBL] [Abstract][Full Text] [Related]  

  • 24. Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and Deep Learning.
    Yang W; Wang J; Zhao L; Chen J
    Molecules; 2024 Jul; 29(14):. PubMed ID: 39064955
    [TBL] [Abstract][Full Text] [Related]  

  • 25. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2.
    Athanasiou C; Vasilakaki S; Dellis D; Cournia Z
    J Comput Aided Mol Des; 2018 Jan; 32(1):21-44. PubMed ID: 29119352
    [TBL] [Abstract][Full Text] [Related]  

  • 26. CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.
    Zhang H; Kim S; Giese TJ; Lee TS; Lee J; York DM; Im W
    J Chem Inf Model; 2021 Sep; 61(9):4145-4151. PubMed ID: 34521199
    [TBL] [Abstract][Full Text] [Related]  

  • 27. Molecular Modeling Investigation of Folic Acid Conjugation to MDM2 Inhibitors for Enhanced Cellular Uptake and Target Binding.
    Patil SP; Kerezsi CR; Hicks BM; Jednorski AH
    Curr Comput Aided Drug Des; 2015; 11(3):258-65. PubMed ID: 26265252
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Calculation of absolute protein-ligand binding constants with the molecular dynamics free energy perturbation method.
    Woo HJ
    Methods Mol Biol; 2008; 443():109-20. PubMed ID: 18446284
    [TBL] [Abstract][Full Text] [Related]  

  • 29. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations.
    Verma S; Grover S; Tyagi C; Goyal S; Jamal S; Singh A; Grover A
    PLoS One; 2016; 11(2):e0149014. PubMed ID: 26863418
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches.
    Miyamoto S; Kollman PA
    Proteins; 1993 Jul; 16(3):226-45. PubMed ID: 8346190
    [TBL] [Abstract][Full Text] [Related]  

  • 31. Combining Alchemical Transformation with a Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites.
    Cruz J; Wickstrom L; Yang D; Gallicchio E; Deng N
    J Chem Theory Comput; 2020 Apr; 16(4):2803-2813. PubMed ID: 32101691
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Accurate calculation of absolute free energy of binding for SHP2 allosteric inhibitors using free energy perturbation.
    Liang L; Liu H; Xing G; Deng C; Hua Y; Gu R; Lu T; Chen Y; Zhang Y
    Phys Chem Chem Phys; 2022 May; 24(17):9904-9920. PubMed ID: 35416820
    [TBL] [Abstract][Full Text] [Related]  

  • 33. A computational analysis of the binding model of MDM2 with inhibitors.
    Hu G; Wang D; Liu X; Zhang Q
    J Comput Aided Mol Des; 2010 Aug; 24(8):687-97. PubMed ID: 20490618
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Accuracy assessment and automation of free energy calculations for drug design.
    Christ CD; Fox T
    J Chem Inf Model; 2014 Jan; 54(1):108-20. PubMed ID: 24256082
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.
    Wang J; Miao Y
    J Chem Theory Comput; 2024 Jul; 20(14):5829-5841. PubMed ID: 39002136
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Inhibitors of MDM2 and MDMX: a structural perspective.
    Riedinger C; McDonnell JM
    Future Med Chem; 2009 Sep; 1(6):1075-94. PubMed ID: 21425995
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations.
    Ben-Shalom IY; Pfeiffer-Marek S; Baringhaus KH; Gohlke H
    J Chem Inf Model; 2017 Feb; 57(2):170-189. PubMed ID: 27996253
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series.
    Sabanés Zariquiey F; Pérez A; Majewski M; Gallicchio E; De Fabritiis G
    J Chem Inf Model; 2023 Apr; 63(8):2438-2444. PubMed ID: 37042797
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3.
    He X; Man VH; Ji B; Xie XQ; Wang J
    J Comput Aided Mol Des; 2019 Jan; 33(1):105-117. PubMed ID: 30218199
    [TBL] [Abstract][Full Text] [Related]  

  • 40. Rapid alchemical free energy calculation employing a generalized born implicit solvent model.
    Ostermeir K; Zacharias M
    J Phys Chem B; 2015 Jan; 119(3):968-75. PubMed ID: 25160060
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 18.