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    Results: 1 to 20 of 93

    1.

    Tetracycline-tet repressor binding specificity: insights from experiments and simulations.

    Aleksandrov A, Schuldt L, Hinrichs W, Simonson T.

    Biophys J. 2009 Nov 18;97(10):2829-38.PMID: 19917238 [PubMed - in process]Related articles

    2.

    Computational design of protein-ligand binding: Modifying the specificity of asparaginyl-tRNA synthetase.

    Lopes A, Busch MS, Simonson T.

    J Comput Chem. 2009 Oct 27. [Epub ahead of print]PMID: 19862811 [PubMed - as supplied by publisher]Related articles

    3.

    Alchemical free energy simulations for biological complexes: powerful but temperamental ...

    Aleksandrov A, Thompson D, Simonson T.

    J Mol Recognit. 2009 Aug 19. [Epub ahead of print]PMID: 19693787 [PubMed - as supplied by publisher]Related articles

    4.

    Genetic adaptation to extreme hypoxia: study of high-altitude pulmonary edema in a three-generation Han Chinese family.

    Lorenzo V F, Yang Y, Simonson TS, Nussenzveig R, Jorde LB, Prchal JT, Ge RL.

    Blood Cells Mol Dis. 2009 Nov-Dec;43(3):221-5. Epub 2009 May 29.PMID: 19481479 [PubMed - in process]Related articles

    5.

    Computational protein design as a tool for fold recognition.

    am Busch MS, Mignon D, Simonson T.

    Proteins. 2009 Oct;77(1):139-58.PMID: 19408297 [PubMed - indexed for MEDLINE]Related articles

    6.

    Bacillus anthracis in China and its relationship to worldwide lineages.

    Simonson TS, Okinaka RT, Wang B, Easterday WR, Huynh L, U'Ren JM, Dukerich M, Zanecki SR, Kenefic LJ, Beaudry J, Schupp JM, Pearson T, Wagner DM, Hoffmaster A, Ravel J, Keim P.

    BMC Microbiol. 2009 Apr 15;9:71.PMID: 19368722 [PubMed - indexed for MEDLINE]Related articlesFree article

    7.

    Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness.

    Noirel J, Simonson T.

    J Chem Phys. 2008 Nov 14;129(18):185104.PMID: 19045432 [PubMed - indexed for MEDLINE]Related articles

    8.

    Binding of tetracyclines to elongation factor Tu, the Tet repressor, and the ribosome: a molecular dynamics simulation study.

    Aleksandrov A, Simonson T.

    Biochemistry. 2008 Dec 23;47(51):13594-603.PMID: 19032078 [PubMed - indexed for MEDLINE]Related articles

    9.

    Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations.

    Launay G, Simonson T.

    BMC Bioinformatics. 2008 Oct 9;9:427.PMID: 18844985 [PubMed - indexed for MEDLINE]Related articlesFree article

    10.

    Molecular mechanics models for tetracycline analogs.

    Aleksandrov A, Simonson T.

    J Comput Chem. 2009 Jan 30;30(2):243-55.PMID: 18615434 [PubMed - indexed for MEDLINE]Related articles

    11.

    Dielectric relaxation in proteins: the computational perspective.

    Simonson T.

    Photosynth Res. 2008 Jul;97(1):21-32. Epub 2008 Apr 29. Review.PMID: 18443919 [PubMed - indexed for MEDLINE]Related articles

    12.

    Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallographic study.

    Aleksandrov A, Schuldt L, Hinrichs W, Simonson T.

    J Mol Biol. 2008 May 9;378(4):898-912. Epub 2008 Mar 19.PMID: 18395746 [PubMed - indexed for MEDLINE]Related articles

    13.

    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.PMID: 18366628 [PubMed - indexed for MEDLINE]Related articlesFree article

    14.

    Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site.

    Aleksandrov A, Simonson T.

    J Am Chem Soc. 2008 Jan 30;130(4):1114-5. No abstract available. PMID: 18219717 [PubMed - indexed for MEDLINE]Related articles

    15.

    Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations.

    Thompson D, Lazennec C, Plateau P, Simonson T.

    Proteins. 2008 May 15;71(3):1450-60.PMID: 18076053 [PubMed - indexed for MEDLINE]Related articles

    16.

    Computational protein design: software implementation, parameter optimization, and performance of a simple model.

    Schmidt Am Busch M, Lopes A, Mignon D, Simonson T.

    J Comput Chem. 2008 May;29(7):1092-102.PMID: 18069664 [PubMed - indexed for MEDLINE]Related articles

    17.

    Neutral evolution of protein-protein interactions: a computational study using simple models.

    Noirel J, Simonson T.

    BMC Struct Biol. 2007 Nov 19;7:79.PMID: 18021454 [PubMed - indexed for MEDLINE]Related articlesFree article

    18.

    Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase.

    Thompson D, Lazennec C, Plateau P, Simonson T.

    J Biol Chem. 2007 Oct 19;282(42):30856-68. Epub 2007 Aug 9.PMID: 17690095 [PubMed - indexed for MEDLINE]Related articlesFree article

    19.

    Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.

    Launay G, Mendez R, Wodak S, Simonson T.

    BMC Bioinformatics. 2007 Jul 27;8:270.PMID: 17662112 [PubMed - indexed for MEDLINE]Related articlesFree article

    20.

    Global genetic population structure of Bacillus anthracis.

    Van Ert MN, Easterday WR, Huynh LY, Okinaka RT, Hugh-Jones ME, Ravel J, Zanecki SR, Pearson T, Simonson TS, U'Ren JM, Kachur SM, Leadem-Dougherty RR, Rhoton SD, Zinser G, Farlow J, Coker PR, Smith KL, Wang B, Kenefic LJ, Fraser-Liggett CM, Wagner DM, Keim P.

    PLoS One. 2007 May 23;2(5):e461.PMID: 17520020 [PubMed]Related articlesFree article

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