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Journal Abstract Search

345 related items for PubMed ID: 16844742

  • 1. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.
    Wang J, Deng Y, Roux B.
    Biophys J; 2006 Oct 15; 91(8):2798-814. PubMed ID: 16844742
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  • 2. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
    Ge X, Roux B.
    J Mol Recognit; 2010 Oct 15; 23(2):128-41. PubMed ID: 20151411
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  • 4. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.
    Jo S, Jiang W, Lee HS, Roux B, Im W.
    J Chem Inf Model; 2013 Jan 28; 53(1):267-77. PubMed ID: 23205773
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  • 7. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations.
    Deng Y, Roux B.
    J Chem Phys; 2008 Mar 21; 128(11):115103. PubMed ID: 18361618
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  • 10. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.
    Shivakumar D, Deng Y, Roux B.
    J Chem Theory Comput; 2009 Apr 14; 5(4):919-30. PubMed ID: 26609601
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  • 11. Accurate and efficient corrections for missing dispersion interactions in molecular simulations.
    Shirts MR, Mobley DL, Chodera JD, Pande VS.
    J Phys Chem B; 2007 Nov 15; 111(45):13052-63. PubMed ID: 17949030
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  • 12. Conformational Entropy of FK506 Binding to FKBP12 Determined by Nuclear Magnetic Resonance Relaxation and Molecular Dynamics Simulations.
    Solomentsev G, Diehl C, Akke M.
    Biochemistry; 2018 Mar 06; 57(9):1451-1461. PubMed ID: 29412644
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  • 13. 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 01; 18(22):15005-18. PubMed ID: 27193181
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  • 14. CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations.
    Kim S, Oshima H, Zhang H, Kern NR, Re S, Lee J, Roux B, Sugita Y, Jiang W, Im W.
    J Chem Theory Comput; 2020 Nov 10; 16(11):7207-7218. PubMed ID: 33112150
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  • 15. Protein-Ligand Binding Free Energy Calculations with FEP.
    Wang L, Chambers J, Abel R.
    Methods Mol Biol; 2019 Nov 10; 2022():201-232. PubMed ID: 31396905
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  • 16. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.
    Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L.
    J Chem Theory Comput; 2015 Jun 09; 11(6):2670-9. PubMed ID: 26085821
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  • 18. Charging free energy calculations using the Generalized Solvent Boundary Potential (GSBP) and periodic boundary condition: a comparative analysis using ion solvation and oxidation free energy in proteins.
    Lu X, Cui Q.
    J Phys Chem B; 2013 Feb 21; 117(7):2005-18. PubMed ID: 23347181
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  • 20. 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 21; 16(3):226-45. PubMed ID: 8346190
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