BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

133 related articles for article (PubMed ID: 23085166)

  • 1. Implementation of the force decomposition machine for molecular dynamics simulations.
    Borštnik U; Miller BT; Brooks BR; Janežič D
    J Mol Graph Model; 2012 Sep; 38():243-7. PubMed ID: 23085166
    [TBL] [Abstract][Full Text] [Related]  

  • 2. The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations.
    Borštnik U; Miller BT; Brooks BR; Janežič D
    J Comput Chem; 2011 Nov; 32(14):3005-13. PubMed ID: 21793007
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field.
    Duan R; Lazim R; Zhang D
    J Comput Chem; 2015 Sep; 36(25):1885-92. PubMed ID: 26198456
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from molecular dynamics.
    Meher BR; Kumar MV; Bandyopadhyay P
    J Biomol Struct Dyn; 2014; 32(6):899-915. PubMed ID: 23782135
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields.
    Meher BR; Kumar MV; Sharma S; Bandyopadhyay P
    J Bioinform Comput Biol; 2012 Dec; 10(6):1250018. PubMed ID: 22845837
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations.
    Li D; Han JG; Chen H; Li L; Zhao RN; Liu G; Duan Y
    J Mol Model; 2012 May; 18(5):1841-54. PubMed ID: 21850570
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design.
    Perryman AL; Lin JH; McCammon JA
    Biopolymers; 2006 Jun; 82(3):272-84. PubMed ID: 16508951
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease.
    Whitfield TW; Ragland DA; Zeldovich KB; Schiffer CA
    J Chem Theory Comput; 2020 Feb; 16(2):1284-1299. PubMed ID: 31877249
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Inhibition of the activity of HIV-1 protease through antibody binding and mutations probed by molecular dynamics simulations.
    Badaya A; Sasidhar YU
    Sci Rep; 2020 Mar; 10(1):5501. PubMed ID: 32218488
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations.
    Jenwitheesuk E; Samudrala R
    BMC Struct Biol; 2003 Apr; 3():2. PubMed ID: 12675950
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis.
    Karnati KR; Wang Y
    J Mol Graph Model; 2019 Nov; 92():112-122. PubMed ID: 31351319
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights.
    Chetty S; Bhakat S; Martin AJ; Soliman ME
    J Biomol Struct Dyn; 2016; 34(1):135-51. PubMed ID: 25671669
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Exploring the drug resistance of V32I and M46L mutant HIV-1 protease to inhibitor TMC114: flap dynamics and binding mechanism.
    Meher BR; Wang Y
    J Mol Graph Model; 2015 Mar; 56():60-73. PubMed ID: 25562662
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies.
    Meher BR; Wang Y
    J Phys Chem B; 2012 Feb; 116(6):1884-900. PubMed ID: 22239286
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Computational Studies of a Mechanism for Binding and Drug Resistance in the Wild Type and Four Mutations of HIV-1 Protease with a GRL-0519 Inhibitor.
    Hu G; Ma A; Dou X; Zhao L; Wang J
    Int J Mol Sci; 2016 May; 17(6):. PubMed ID: 27240358
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Comprehensive bioinformatic analysis of the specificity of human immunodeficiency virus type 1 protease.
    You L; Garwicz D; Rögnvaldsson T
    J Virol; 2005 Oct; 79(19):12477-86. PubMed ID: 16160175
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.
    Deng NJ; Zheng W; Gallicchio E; Levy RM
    J Am Chem Soc; 2011 Jun; 133(24):9387-94. PubMed ID: 21561098
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Molecular dynamics applied in drug discovery: the case of HIV-1 protease.
    Shang Y; Simmerling C
    Methods Mol Biol; 2012; 819():527-49. PubMed ID: 22183556
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA-approved inhibitors: MD study.
    Maphumulo SI; Halder AK; Govender T; Maseko S; Maguire GEM; Honarparvar B; Kruger HG
    Chem Biol Drug Des; 2018 Nov; 92(5):1899-1913. PubMed ID: 30003668
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Heterogeneous CPU+GPU-Enabled Simulations for DFTB Molecular Dynamics of Large Chemical and Biological Systems.
    Allec SI; Sun Y; Sun J; Chang CA; Wong BM
    J Chem Theory Comput; 2019 May; 15(5):2807-2815. PubMed ID: 30916958
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.