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219 related items for PubMed ID: 11565842

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

  • 2. Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations.
    Kurt N, Scott WR, Schiffer CA, Haliloglu T.
    Proteins; 2003 May 15; 51(3):409-22. PubMed ID: 12696052
    [Abstract] [Full Text] [Related]

  • 3. 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]

  • 4. A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment.
    Lounnas V, Pettitt BM.
    Proteins; 1994 Feb 15; 18(2):133-47. PubMed ID: 8159663
    [Abstract] [Full Text] [Related]

  • 5. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
    Hassan SA, Mehler EL, Zhang D, Weinstein H.
    Proteins; 2003 Apr 01; 51(1):109-25. PubMed ID: 12596268
    [Abstract] [Full Text] [Related]

  • 6. Dynamics of hydration in hen egg white lysozyme.
    Sterpone F, Ceccarelli M, Marchi M.
    J Mol Biol; 2001 Aug 10; 311(2):409-19. PubMed ID: 11478869
    [Abstract] [Full Text] [Related]

  • 7. Multiple solvent crystal structures of ribonuclease A: an assessment of the method.
    Dechene M, Wink G, Smith M, Swartz P, Mattos C.
    Proteins; 2009 Sep 10; 76(4):861-81. PubMed ID: 19291738
    [Abstract] [Full Text] [Related]

  • 8. Extracting hydration sites around proteins from explicit water simulations.
    Henchman RH, McCammon JA.
    J Comput Chem; 2002 Jul 15; 23(9):861-9. PubMed ID: 11984847
    [Abstract] [Full Text] [Related]

  • 9. Dynamics of the native and the ligand-bound structures of eosinophil cationic protein: network of hydrogen bonds at the catalytic site.
    Sanjeev BS, Vishveshwara S.
    J Biomol Struct Dyn; 2005 Jun 15; 22(6):657-72. PubMed ID: 15842171
    [Abstract] [Full Text] [Related]

  • 10. Protein-water interactions in ribonuclease A and angiogenin: a molecular dynamics study.
    Sanjeev BS, Vishveshwara S.
    Proteins; 2004 Jun 01; 55(4):915-23. PubMed ID: 15146489
    [Abstract] [Full Text] [Related]

  • 11. Structural characteristics of hydration sites in lysozyme.
    Soda K, Shimbo Y, Seki Y, Taiji M.
    Biophys Chem; 2011 Jun 01; 156(1):31-42. PubMed ID: 21435773
    [Abstract] [Full Text] [Related]

  • 12. Comparison of the dynamics of bovine and human angiogenin: a molecular dynamics study.
    Madhusudhan MS, Vishveshwara S.
    Biopolymers; 1999 Feb 01; 49(2):131-44. PubMed ID: 10070263
    [Abstract] [Full Text] [Related]

  • 13. Static and dynamic water molecules in Cu,Zn superoxide dismutase.
    Falconi M, Brunelli M, Pesce A, Ferrario M, Bolognesi M, Desideri A.
    Proteins; 2003 Jun 01; 51(4):607-15. PubMed ID: 12784219
    [Abstract] [Full Text] [Related]

  • 14. Protein hinge bending as seen in molecular dynamics simulations of native and M61 mutant T4 lysozymes.
    Arnold GE, Ornstein RL.
    Biopolymers; 1997 Apr 15; 41(5):533-44. PubMed ID: 9095676
    [Abstract] [Full Text] [Related]

  • 15. Effect of alcohols on protein hydration: crystallographic analysis of hen egg-white lysozyme in the presence of alcohols.
    Deshpande A, Nimsadkar S, Mande SC.
    Acta Crystallogr D Biol Crystallogr; 2005 Jul 15; 61(Pt 7):1005-8. PubMed ID: 15983424
    [Abstract] [Full Text] [Related]

  • 16. 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]

  • 17. Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole.
    Higo J, Nakasako M.
    J Comput Chem; 2002 Nov 15; 23(14):1323-36. PubMed ID: 12214315
    [Abstract] [Full Text] [Related]

  • 18. NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex.
    Tsui V, Radhakrishnan I, Wright PE, Case DA.
    J Mol Biol; 2000 Oct 06; 302(5):1101-17. PubMed ID: 11183777
    [Abstract] [Full Text] [Related]

  • 19. Molecular dynamics simulations of ligand-induced flap closing in HIV-1 protease approach X-ray resolution: establishing the role of bound water in the flap closing mechanism.
    Singh G, Senapati S.
    Biochemistry; 2008 Oct 07; 47(40):10657-64. PubMed ID: 18785756
    [Abstract] [Full Text] [Related]

  • 20. Translational and rotational diffusion of proteins.
    Smith PE, van Gunsteren WF.
    J Mol Biol; 1994 Feb 18; 236(2):629-36. PubMed ID: 7508990
    [Abstract] [Full Text] [Related]

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