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 *

464 related articles for article (PubMed ID: 19778066)

  • 1. Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization.
    Michel J; Tirado-Rives J; Jorgensen WL
    J Am Chem Soc; 2009 Oct; 131(42):15403-11. PubMed ID: 19778066
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Evaluation of water displacement energetics in protein binding sites with grid cell theory.
    Gerogiokas G; Southey MW; Mazanetz MP; Heifetz A; Bodkin M; Law RJ; Michel J
    Phys Chem Chem Phys; 2015 Apr; 17(13):8416-26. PubMed ID: 25600031
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations.
    Bruce Macdonald HE; Cave-Ayland C; Ross GA; Essex JW
    J Chem Theory Comput; 2018 Dec; 14(12):6586-6597. PubMed ID: 30451501
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Prediction of the water content in protein binding sites.
    Michel J; Tirado-Rives J; Jorgensen WL
    J Phys Chem B; 2009 Oct; 113(40):13337-46. PubMed ID: 19754086
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Binding dynamics of two water molecules constrained within the scytalone dehydratase binding pocket.
    Jordan DB; Basarab GS
    Bioorg Med Chem Lett; 2000 Jan; 10(1):23-6. PubMed ID: 10636235
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Hydration properties of ligands and drugs in protein binding sites: tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies.
    García-Sosa AT
    J Chem Inf Model; 2013 Jun; 53(6):1388-405. PubMed ID: 23662606
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations.
    Wahl J; Smieško M
    ChemMedChem; 2018 Jul; 13(13):1325-1335. PubMed ID: 29726604
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy.
    Gauto DF; Di Lella S; Guardia CM; Estrin DA; Martí MA
    J Phys Chem B; 2009 Jun; 113(25):8717-24. PubMed ID: 19485380
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Effective lead optimization targeting the displacement of bridging receptor-ligand water molecules.
    Chen D; Li Y; Zhao M; Tan W; Li X; Savidge T; Guo W; Fan X
    Phys Chem Chem Phys; 2018 Oct; 20(37):24399-24407. PubMed ID: 30221291
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Calculation of Thermodynamic Properties of Bound Water Molecules.
    Yang Y; Abdallah AHA; Lill MA
    Methods Mol Biol; 2018; 1762():389-402. PubMed ID: 29594782
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method.
    Lukac I; Wyatt PG; Gilbert IH; Zuccotto F
    J Comput Aided Mol Des; 2021 Oct; 35(10):1025-1036. PubMed ID: 34458939
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks.
    Rudling A; Orro A; Carlsson J
    J Chem Inf Model; 2018 Feb; 58(2):350-361. PubMed ID: 29308882
    [TBL] [Abstract][Full Text] [Related]  

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

  • 14. The effect of water displacement on binding thermodynamics: concanavalin A.
    Li Z; Lazaridis T
    J Phys Chem B; 2005 Jan; 109(1):662-70. PubMed ID: 16851059
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase.
    Okimoto N; Nakamura T; Suenaga A; Futatsugi N; Hirano Y; Yamaguchi I; Ebisuzaki T
    J Am Chem Soc; 2004 Oct; 126(40):13132-9. PubMed ID: 15469312
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series.
    Güssregen S; Matter H; Hessler G; Lionta E; Heil J; Kast SM
    J Chem Inf Model; 2017 Jul; 57(7):1652-1666. PubMed ID: 28565907
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.
    Ben-Shalom IY; Lin Z; Radak BK; Lin C; Sherman W; Gilson MK
    J Chem Theory Comput; 2020 Dec; 16(12):7883-7894. PubMed ID: 33206520
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Methyl effects on protein-ligand binding.
    Leung CS; Leung SS; Tirado-Rives J; Jorgensen WL
    J Med Chem; 2012 May; 55(9):4489-500. PubMed ID: 22500930
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Involvement of water in carbohydrate-protein binding: concanavalin A revisited.
    Kadirvelraj R; Foley BL; Dyekjaer JD; Woods RJ
    J Am Chem Soc; 2008 Dec; 130(50):16933-42. PubMed ID: 19053475
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors.
    Pearlstein RA; Sherman W; Abel R
    Proteins; 2013 Sep; 81(9):1509-26. PubMed ID: 23468227
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 24.