Andrei L Lomize

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. pmc OPM database and PPM web server: resources for positioning of proteins in membranes
    Mikhail A Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109 1065 USA
    Nucleic Acids Res 40:D370-6. 2012
  2. ncbi request reprint Prediction of protein structure: the problem of fold multiplicity
    A L Lomize
    College of Pharmacy, University of Michigan, Ann Arbor 48109, USA
    Proteins . 1999
  3. pmc Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects
    Andrei L Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St, Ann Arbor, Michigan 48109 1065, USA
    J Chem Inf Model 51:918-29. 2011
  4. pmc Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes
    Andrei L Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St, Ann Arbor, Michigan 48109 1065, USA
    J Chem Inf Model 51:930-46. 2011
  5. pmc The role of hydrophobic interactions in positioning of peripheral proteins in membranes
    Andrei L Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109 1065, USA
    BMC Struct Biol 7:44. 2007
  6. pmc Positioning of proteins in membranes: a computational approach
    Andrei L Lomize
    College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109 1065, USA
    Protein Sci 15:1318-33. 2006
  7. pmc Quantification of helix-helix binding affinities in micelles and lipid bilayers
    Andrei L Lomize
    College of Pharmacy, University of Michigan, 428 Church St, Ann Arbor, MI 48109 1065, USA
    Protein Sci 13:2600-12. 2004
  8. pmc Interatomic potentials and solvation parameters from protein engineering data for buried residues
    Andrei L Lomize
    College of Pharmacy, University of Michigan, Ann Arbor 48109 1065, USA
    Protein Sci 11:1984-2000. 2002
  9. ncbi request reprint OPM: orientations of proteins in membranes database
    Mikhail A Lomize
    College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI 48109 1065, USA
    Bioinformatics 22:623-5. 2006
  10. doi request reprint Solvation models and computational prediction of orientations of peptides and proteins in membranes
    Andrei L Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
    Methods Mol Biol 1063:125-42. 2013

Detail Information

Publications13

  1. pmc OPM database and PPM web server: resources for positioning of proteins in membranes
    Mikhail A Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109 1065 USA
    Nucleic Acids Res 40:D370-6. 2012
    ..The database is supplemented by the PPM server (http://opm.phar.umich.edu/server.php) which can be used for calculating spatial positions in membranes of newly determined proteins structures or theoretical models...
  2. ncbi request reprint Prediction of protein structure: the problem of fold multiplicity
    A L Lomize
    College of Pharmacy, University of Michigan, Ann Arbor 48109, USA
    Proteins . 1999
    ....
  3. pmc Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects
    Andrei L Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St, Ann Arbor, Michigan 48109 1065, USA
    J Chem Inf Model 51:918-29. 2011
    ..The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes...
  4. pmc Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes
    Andrei L Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St, Ann Arbor, Michigan 48109 1065, USA
    J Chem Inf Model 51:930-46. 2011
    ..The results of calculations are deposited in the updated OPM database ( http://opm.phar.umich.edu )...
  5. pmc The role of hydrophobic interactions in positioning of peripheral proteins in membranes
    Andrei L Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109 1065, USA
    BMC Struct Biol 7:44. 2007
    ..Biological activity, stability, and conformations of these proteins depend on their spatial positions with respect to the lipid bilayer. However, these positions are usually undetermined...
  6. pmc Positioning of proteins in membranes: a computational approach
    Andrei L Lomize
    College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109 1065, USA
    Protein Sci 15:1318-33. 2006
    ..Coordinates of all studied proteins with their membrane boundaries can be found in the Orientations of Proteins in Membranes (OPM) database:http://opm.phar.umich.edu/...
  7. pmc Quantification of helix-helix binding affinities in micelles and lipid bilayers
    Andrei L Lomize
    College of Pharmacy, University of Michigan, 428 Church St, Ann Arbor, MI 48109 1065, USA
    Protein Sci 13:2600-12. 2004
    ..The energetics of amino acid substitutions in bacteriorhodopsin was complicated by specific binding of lipid and water molecules to cavities created in certain mutants...
  8. pmc Interatomic potentials and solvation parameters from protein engineering data for buried residues
    Andrei L Lomize
    College of Pharmacy, University of Michigan, Ann Arbor 48109 1065, USA
    Protein Sci 11:1984-2000. 2002
    ..An analysis of additional replacements at the water-protein interface indicates that vdW interactions between protein atoms are reduced when they occur across water...
  9. ncbi request reprint OPM: orientations of proteins in membranes database
    Mikhail A Lomize
    College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI 48109 1065, USA
    Bioinformatics 22:623-5. 2006
    ..All coordinate files with the calculated membrane boundaries are available for downloading...
  10. doi request reprint Solvation models and computational prediction of orientations of peptides and proteins in membranes
    Andrei L Lomize
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
    Methods Mol Biol 1063:125-42. 2013
    ....
  11. pmc Structural adaptations of proteins to different biological membranes
    Irina D Pogozheva
    College of Pharmacy, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109 1065, USA Electronic address
    Biochim Biophys Acta 1828:2592-608. 2013
    ..In artificial lipid bilayers, midpolar regions are observed up to the level of acyl chain double bonds. ..
  12. pmc Interactions of human melanocortin 4 receptor with nonpeptide and peptide agonists
    Irina D Pogozheva
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, USA
    Biochemistry 44:11329-41. 2005
    ....
  13. ncbi request reprint Complex of an active mu-opioid receptor with a cyclic peptide agonist modeled from experimental constraints
    Carol B Fowler
    Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109 1065, USA
    Biochemistry 43:15796-810. 2004
    ..In the active state, the binding pocket of the mu-receptor is complementary to the previously proposed receptor-bound conformation of JOM6...