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Journal Abstract Search

103 related items for PubMed ID: 21916516

  • 1. Probing the dynamic nature of water molecules and their influences on ligand binding in a model binding site.
    Cappel D, Wahlström R, Brenk R, Sotriffer CA.
    J Chem Inf Model; 2011 Oct 24; 51(10):2581-94. PubMed ID: 21916516
    [Abstract] [Full Text] [Related]

  • 2. Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations.
    Baron R, McCammon JA.
    Biochemistry; 2007 Sep 18; 46(37):10629-42. PubMed ID: 17718514
    [Abstract] [Full Text] [Related]

  • 3. Small molecule binding to an artificially created cavity at the active site of cytochrome c peroxidase.
    Fitzgerald MM, Churchill MJ, McRee DE, Goodin DB.
    Biochemistry; 1994 Apr 05; 33(13):3807-18. PubMed ID: 8142383
    [Abstract] [Full Text] [Related]

  • 4. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding.
    Baron R, McCammon JA.
    Chemphyschem; 2008 May 16; 9(7):983-8. PubMed ID: 18418822
    [Abstract] [Full Text] [Related]

  • 5. Structural and dynamic roles of permanent water molecules in ligand molecular recognition by chicken liver bile acid binding protein.
    Ricchiuto P, Rocco AG, Gianazza E, Corrada D, Beringhelli T, Eberini I.
    J Mol Recognit; 2008 May 16; 21(5):348-54. PubMed ID: 18654997
    [Abstract] [Full Text] [Related]

  • 6. Cytochrome c/cytochrome c peroxidase complex: effect of binding-site mutations on the thermodynamics of complex formation.
    Erman JE, Kresheck GC, Vitello LB, Miller MA.
    Biochemistry; 1997 Apr 01; 36(13):4054-60. PubMed ID: 9092837
    [Abstract] [Full Text] [Related]

  • 7. Probing molecular docking in a charged model binding site.
    Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK.
    J Mol Biol; 2006 Apr 14; 357(5):1449-70. PubMed ID: 16490206
    [Abstract] [Full Text] [Related]

  • 8. Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein.
    Musah RA, Jensen GM, Bunte SW, Rosenfeld RJ, Goodin DB.
    J Mol Biol; 2002 Jan 25; 315(4):845-57. PubMed ID: 11812152
    [Abstract] [Full Text] [Related]

  • 9. Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules.
    Amadasi A, Spyrakis F, Cozzini P, Abraham DJ, Kellogg GE, Mozzarelli A.
    J Mol Biol; 2006 Apr 21; 358(1):289-309. PubMed ID: 16497327
    [Abstract] [Full Text] [Related]

  • 10. A comparative analysis of the role of water in the binding pockets of ionotropic glutamate receptors.
    Vijayan R, Sahai MA, Czajkowski T, Biggin PC.
    Phys Chem Chem Phys; 2010 Nov 14; 12(42):14057-66. PubMed ID: 20856958
    [Abstract] [Full Text] [Related]

  • 11. Molecular dynamics study of water penetration in staphylococcal nuclease.
    Damjanović A, García-Moreno B, Lattman EE, García AE.
    Proteins; 2005 Aug 15; 60(3):433-49. PubMed ID: 15971206
    [Abstract] [Full Text] [Related]

  • 12. Quantum mechanics/molecular mechanics strategies for docking pose refinement: distinguishing between binders and decoys in cytochrome C peroxidase.
    Burger SK, Thompson DC, Ayers PW.
    J Chem Inf Model; 2011 Jan 24; 51(1):93-101. PubMed ID: 21133348
    [Abstract] [Full Text] [Related]

  • 13. Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c.
    Payne TM, Yee EF, Dzikovski B, Crane BR.
    Biochemistry; 2016 Aug 30; 55(34):4807-22. PubMed ID: 27499202
    [Abstract] [Full Text] [Related]

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  • 16. Effect of single-site charge-reversal mutations on the catalytic properties of yeast cytochrome c peroxidase: evidence for a single, catalytically active, cytochrome c binding domain.
    Pearl NM, Jacobson T, Meyen C, Clementz AG, Ok EY, Choi E, Wilson K, Vitello LB, Erman JE.
    Biochemistry; 2008 Mar 04; 47(9):2766-75. PubMed ID: 18232645
    [Abstract] [Full Text] [Related]

  • 17. Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica.
    Koellner G, Kryger G, Millard CB, Silman I, Sussman JL, Steiner T.
    J Mol Biol; 2000 Feb 18; 296(2):713-35. PubMed ID: 10669619
    [Abstract] [Full Text] [Related]

  • 18. Deducing hydration sites of a protein from molecular dynamics simulations.
    Madhusudhan MS, Vishveshwara S.
    J Biomol Struct Dyn; 2001 Aug 18; 19(1):105-14. PubMed ID: 11565842
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