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 *

139 related articles for article (PubMed ID: 22920218)

  • 1. Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities.
    Fuller JC; Jackson RM; Shirts MR
    J Phys Chem B; 2012 Sep; 116(35):10856-69. PubMed ID: 22920218
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.
    Fuller JC; Jackson RM; Edwards TA; Wilson AJ; Shirts MR
    PLoS One; 2012; 7(8):e43253. PubMed ID: 22916232
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface.
    Min D; Li H; Li G; Bitetti-Putzer R; Yang W
    J Chem Phys; 2007 Apr; 126(14):144109. PubMed ID: 17444703
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods.
    Lu N; Kofke DA; Woolf TB
    J Comput Chem; 2004 Jan; 25(1):28-39. PubMed ID: 14634991
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Computation of the binding affinities of catechol-O-methyltransferase inhibitors: multisubstate relative free energy calculations.
    Palma PN; Bonifácio MJ; Loureiro AI; Soares-da-Silva P
    J Comput Chem; 2012 Apr; 33(9):970-86. PubMed ID: 22278964
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Combining ab initio quantum mechanics with a dipole-field model to describe acid dissociation reactions in water: first-principles free energy and entropy calculations.
    Maurer P; Iftimie R
    J Chem Phys; 2010 Feb; 132(7):074112. PubMed ID: 20170220
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.
    Archontis G; Simonson T; Karplus M
    J Mol Biol; 2001 Feb; 306(2):307-27. PubMed ID: 11237602
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.
    Genheden S; Nilsson I; Ryde U
    J Chem Inf Model; 2011 Apr; 51(4):947-58. PubMed ID: 21417269
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Understanding microscopic binding of macrophage migration inhibitory factor with phenolic hydrazones by molecular docking, molecular dynamics simulations and free energy calculations.
    Xu L; Li Y; Li L; Zhou S; Hou T
    Mol Biosyst; 2012 Sep; 8(9):2260-73. PubMed ID: 22739754
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.
    Zhang I; Rufa DA; Pulido I; Henry MM; Rosen LE; Hauser K; Singh S; Chodera JD
    J Chem Theory Comput; 2023 Aug; 19(15):4863-4882. PubMed ID: 37450482
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space.
    Kim I; Allen TW
    J Chem Phys; 2012 Apr; 136(16):164103. PubMed ID: 22559466
    [TBL] [Abstract][Full Text] [Related]  

  • 13. A large-scale test of free-energy simulation estimates of protein-ligand binding affinities.
    Mikulskis P; Genheden S; Ryde U
    J Chem Inf Model; 2014 Oct; 54(10):2794-806. PubMed ID: 25264937
    [TBL] [Abstract][Full Text] [Related]  

  • 14. A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies.
    Woods CJ; Malaisree M; Hannongbua S; Mulholland AJ
    J Chem Phys; 2011 Feb; 134(5):054114. PubMed ID: 21303099
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics.
    Jayachandran G; Shirts MR; Park S; Pande VS
    J Chem Phys; 2006 Aug; 125(8):084901. PubMed ID: 16965051
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Enhanced ligand sampling for relative protein-ligand binding free energy calculations.
    Kaus JW; McCammon JA
    J Phys Chem B; 2015 May; 119(20):6190-7. PubMed ID: 25906170
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Incorporating receptor flexibility in the molecular design of protein interfaces.
    Li L; Liang S; Pilcher MM; Meroueh SO
    Protein Eng Des Sel; 2009 Sep; 22(9):575-86. PubMed ID: 19643976
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Docking study and free energy simulation of the complex between p53 DNA-binding domain and azurin.
    De Grandis V; Bizzarri AR; Cannistraro S
    J Mol Recognit; 2007; 20(4):215-26. PubMed ID: 17703463
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Free energy calculations of protein-ligand interactions.
    de Ruiter A; Oostenbrink C
    Curr Opin Chem Biol; 2011 Aug; 15(4):547-52. PubMed ID: 21684797
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study.
    Aldeghi M; Bodkin MJ; Knapp S; Biggin PC
    J Chem Inf Model; 2017 Sep; 57(9):2203-2221. PubMed ID: 28786670
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.