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Journal Abstract Search

153 related items for PubMed ID: 17348031

  • 1. Computational sidechain placement and protein mutagenesis with implicit solvent models.
    Lopes A, Alexandrov A, Bathelt C, Archontis G, Simonson T.
    Proteins; 2007 Jun 01; 67(4):853-67. PubMed ID: 17348031
    [Abstract] [Full Text] [Related]

  • 2. Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.
    am Busch MS, Lopes A, Amara N, Bathelt C, Simonson T.
    BMC Bioinformatics; 2008 Mar 13; 9():148. PubMed ID: 18366628
    [Abstract] [Full Text] [Related]

  • 3. Generalized born model with a simple smoothing function.
    Im W, Lee MS, Brooks CL.
    J Comput Chem; 2003 Nov 15; 24(14):1691-702. PubMed ID: 12964188
    [Abstract] [Full Text] [Related]

  • 4. FACTS: Fast analytical continuum treatment of solvation.
    Haberthür U, Caflisch A.
    J Comput Chem; 2008 Apr 15; 29(5):701-15. PubMed ID: 17918282
    [Abstract] [Full Text] [Related]

  • 5. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.
    Marenich AV, Cramer CJ, Truhlar DG.
    J Phys Chem B; 2009 May 07; 113(18):6378-96. PubMed ID: 19366259
    [Abstract] [Full Text] [Related]

  • 6. A residue-pairwise generalized born scheme suitable for protein design calculations.
    Archontis G, Simonson T.
    J Phys Chem B; 2005 Dec 01; 109(47):22667-73. PubMed ID: 16853951
    [Abstract] [Full Text] [Related]

  • 7. Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
    Simonson T, Carlsson J, Case DA.
    J Am Chem Soc; 2004 Apr 07; 126(13):4167-80. PubMed ID: 15053606
    [Abstract] [Full Text] [Related]

  • 8. A new implicit solvent model for protein-ligand docking.
    Morreale A, Gil-Redondo R, Ortiz AR.
    Proteins; 2007 May 15; 67(3):606-16. PubMed ID: 17330937
    [Abstract] [Full Text] [Related]

  • 9. Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.
    Olson MA.
    Proteins; 2004 Dec 01; 57(4):645-50. PubMed ID: 15481087
    [Abstract] [Full Text] [Related]

  • 10. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.
    Chen J, Brooks CL.
    Phys Chem Chem Phys; 2008 Jan 28; 10(4):471-81. PubMed ID: 18183310
    [Abstract] [Full Text] [Related]

  • 11. Calculation of absolute ligand binding free energy to a ribosome-targeting protein as a function of solvent model.
    Lee MS, Olson MA.
    J Phys Chem B; 2008 Oct 23; 112(42):13411-7. PubMed ID: 18821791
    [Abstract] [Full Text] [Related]

  • 12. AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.
    Gallicchio E, Levy RM.
    J Comput Chem; 2004 Mar 23; 25(4):479-99. PubMed ID: 14735568
    [Abstract] [Full Text] [Related]

  • 13. Energetic decomposition with the generalized-born and Poisson-Boltzmann solvent models: lessons from association of G-protein components.
    Carrascal N, Green DF.
    J Phys Chem B; 2010 Apr 22; 114(15):5096-116. PubMed ID: 20355699
    [Abstract] [Full Text] [Related]

  • 14. Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models.
    Yeh IC, Lee MS, Olson MA.
    J Phys Chem B; 2008 Nov 27; 112(47):15064-73. PubMed ID: 18959439
    [Abstract] [Full Text] [Related]

  • 15. Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity.
    Pokala N, Handel TM.
    J Mol Biol; 2005 Mar 18; 347(1):203-27. PubMed ID: 15733929
    [Abstract] [Full Text] [Related]

  • 16. An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design.
    Vizcarra CL, Zhang N, Marshall SA, Wingreen NS, Zeng C, Mayo SL.
    J Comput Chem; 2008 May 18; 29(7):1153-62. PubMed ID: 18074340
    [Abstract] [Full Text] [Related]

  • 17. Hydrophobic potential of mean force as a solvation function for protein structure prediction.
    Lin MS, Fawzi NL, Head-Gordon T.
    Structure; 2007 Jun 18; 15(6):727-40. PubMed ID: 17562319
    [Abstract] [Full Text] [Related]

  • 18. Electrostatics calculations: latest methodological advances.
    Koehl P.
    Curr Opin Struct Biol; 2006 Apr 18; 16(2):142-51. PubMed ID: 16540310
    [Abstract] [Full Text] [Related]

  • 19. Theory and applications of the generalized Born solvation model in macromolecular simulations.
    Tsui V, Case DA.
    Biopolymers; 2006 Apr 18; 56(4):275-91. PubMed ID: 11754341
    [Abstract] [Full Text] [Related]

  • 20. Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations.
    Kuhn B, Kollman PA, Stahl M.
    J Comput Chem; 2004 Nov 30; 25(15):1865-72. PubMed ID: 15376253
    [Abstract] [Full Text] [Related]

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