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Journal Abstract Search

720 related items for PubMed ID: 25625324

  • 1. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.
    Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R.
    J Am Chem Soc; 2015 Feb 25; 137(7):2695-703. PubMed ID: 25625324
    [Abstract] [Full Text] [Related]

  • 2. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.
    Cournia Z, Allen B, Sherman W.
    J Chem Inf Model; 2017 Dec 26; 57(12):2911-2937. PubMed ID: 29243483
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  • 3. Protein-Ligand Binding Free Energy Calculations with FEP.
    Wang L, Chambers J, Abel R.
    Methods Mol Biol; 2019 Dec 26; 2022():201-232. PubMed ID: 31396905
    [Abstract] [Full Text] [Related]

  • 4. Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms.
    Cavalli A, Spitaleri A, Saladino G, Gervasio FL.
    Acc Chem Res; 2015 Feb 17; 48(2):277-85. PubMed ID: 25496113
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  • 6. Accurate Binding Free Energy Predictions in Fragment Optimization.
    Steinbrecher TB, Dahlgren M, Cappel D, Lin T, Wang L, Krilov G, Abel R, Friesner R, Sherman W.
    J Chem Inf Model; 2015 Nov 23; 55(11):2411-20. PubMed ID: 26457994
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  • 12. Accuracy assessment and automation of free energy calculations for drug design.
    Christ CD, Fox T.
    J Chem Inf Model; 2014 Jan 27; 54(1):108-20. PubMed ID: 24256082
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  • 13. 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 Jan 27; 819():469-86. PubMed ID: 22183552
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  • 14. A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.
    Estrada T, Zhang B, Cicotti P, Armen RS, Taufer M.
    Comput Biol Med; 2012 Jul 27; 42(7):758-71. PubMed ID: 22658682
    [Abstract] [Full Text] [Related]

  • 15. Linear interaction energy: method and applications in drug design.
    Gutiérrez-de-Terán H, Aqvist J.
    Methods Mol Biol; 2012 Jul 27; 819():305-23. PubMed ID: 22183545
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  • 16. A semiempirical free energy force field with charge-based desolvation.
    Huey R, Morris GM, Olson AJ, Goodsell DS.
    J Comput Chem; 2007 Apr 30; 28(6):1145-52. PubMed ID: 17274016
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  • 17. Calculation of absolute protein-ligand binding constants with the molecular dynamics free energy perturbation method.
    Woo HJ.
    Methods Mol Biol; 2008 Apr 30; 443():109-20. PubMed ID: 18446284
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  • 18. Towards predictive ligand design with free-energy based computational methods?
    Foloppe N, Hubbard R.
    Curr Med Chem; 2006 Apr 30; 13(29):3583-608. PubMed ID: 17168725
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  • 19. 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
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  • 20. 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]

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