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.


Pubmed for Handhelds

PUBMED FOR HANDHELDS

Journal Abstract Search

209 related items for PubMed ID: 21684797

  • 1. 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
    [Abstract] [Full Text] [Related]

  • 2. 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 07; 134(5):054114. PubMed ID: 21303099
    [Abstract] [Full Text] [Related]

  • 3. Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.
    Bryce RA.
    Future Med Chem; 2011 Apr 07; 3(6):683-98. PubMed ID: 21554075
    [Abstract] [Full Text] [Related]

  • 4. Calculation of binding free energies of inhibitors to plasmepsin II.
    Steiner D, Oostenbrink C, Diederich F, Zürcher M, van Gunsteren WF.
    J Comput Chem; 2011 Jul 15; 32(9):1801-12. PubMed ID: 21488062
    [Abstract] [Full Text] [Related]

  • 5. Calculation of absolute protein-ligand binding constants with the molecular dynamics free energy perturbation method.
    Woo HJ.
    Methods Mol Biol; 2008 Jul 15; 443():109-20. PubMed ID: 18446284
    [Abstract] [Full Text] [Related]

  • 6. Calculation of absolute protein-ligand binding free energy using distributed replica sampling.
    Rodinger T, Howell PL, Pomès R.
    J Chem Phys; 2008 Oct 21; 129(15):155102. PubMed ID: 19045232
    [Abstract] [Full Text] [Related]

  • 7. Fragment-based computation of binding free energies by systematic sampling.
    Clark M, Meshkat S, Talbot GT, Carnevali P, Wiseman JS.
    J Chem Inf Model; 2009 Aug 21; 49(8):1901-13. PubMed ID: 19610599
    [Abstract] [Full Text] [Related]

  • 8. Protein-Ligand Binding Free Energy Calculations with FEP.
    Wang L, Chambers J, Abel R.
    Methods Mol Biol; 2019 Aug 21; 2022():201-232. PubMed ID: 31396905
    [Abstract] [Full Text] [Related]

  • 9. Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.
    Steinbrecher T, Mobley DL, Case DA.
    J Chem Phys; 2007 Dec 07; 127(21):214108. PubMed ID: 18067350
    [Abstract] [Full Text] [Related]

  • 10. 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 22; 123(8):084108. PubMed ID: 16164283
    [Abstract] [Full Text] [Related]

  • 11. Classification of water molecules in protein binding sites.
    Barillari C, Taylor J, Viner R, Essex JW.
    J Am Chem Soc; 2007 Mar 07; 129(9):2577-87. PubMed ID: 17288418
    [Abstract] [Full Text] [Related]

  • 12. Free energy calculations applied to membrane proteins.
    Chipot C.
    Methods Mol Biol; 2008 Mar 07; 443():121-44. PubMed ID: 18446285
    [Abstract] [Full Text] [Related]

  • 13. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
    Sham YY, Chu ZT, Tao H, Warshel A.
    Proteins; 2000 Jun 01; 39(4):393-407. PubMed ID: 10813821
    [Abstract] [Full Text] [Related]

  • 14. Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors.
    Riniker S, Christ CD, Hansen N, Mark AE, Nair PC, van Gunsteren WF.
    J Chem Phys; 2011 Jul 14; 135(2):024105. PubMed ID: 21766923
    [Abstract] [Full Text] [Related]

  • 15. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.
    Lawrenz M, Baron R, Wang Y, McCammon JA.
    Methods Mol Biol; 2012 Jul 14; 819():469-86. PubMed ID: 22183552
    [Abstract] [Full Text] [Related]

  • 16. Ab initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations.
    Kokubo H, Tanaka T, Okamoto Y.
    J Comput Chem; 2011 Oct 14; 32(13):2810-21. PubMed ID: 21710634
    [Abstract] [Full Text] [Related]

  • 17. Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation.
    Pei J, Wang Q, Zhou J, Lai L.
    Proteins; 2004 Dec 01; 57(4):651-64. PubMed ID: 15390269
    [Abstract] [Full Text] [Related]

  • 18. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.
    Naïm M, Bhat S, Rankin KN, Dennis S, Chowdhury SF, Siddiqi I, Drabik P, Sulea T, Bayly CI, Jakalian A, Purisima EO.
    J Chem Inf Model; 2007 Dec 01; 47(1):122-33. PubMed ID: 17238257
    [Abstract] [Full Text] [Related]

  • 19. Protein-ligand binding free energy calculation by the Smooth Reaction Path Generation (SRPG) Method.
    Fukunishi Y, Mitomo D, Nakamura H.
    J Chem Inf Model; 2009 Aug 01; 49(8):1944-51. PubMed ID: 19807195
    [Abstract] [Full Text] [Related]

  • 20. An all atom energy based computational protocol for predicting binding affinities of protein-ligand complexes.
    Jain T, Jayaram B.
    FEBS Lett; 2005 Dec 05; 579(29):6659-66. PubMed ID: 16307743
    [Abstract] [Full Text] [Related]

    Page: [Next] [New Search]
    of 11.