Andrei L Lomize

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. ncbi 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 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi Prediction of protein structure: the problem of fold multiplicity
    A L Lomize
    College of Pharmacy, University of Michigan, Ann Arbor 48109, USA
    Proteins . 1999
  7. ncbi 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. ncbi 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 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. ncbi 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

Collaborators

Detail Information

Publications11

  1. ncbi 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 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...
  3. ncbi 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 )...
  4. ncbi 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...
  5. ncbi 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/...
  6. ncbi Prediction of protein structure: the problem of fold multiplicity
    A L Lomize
    College of Pharmacy, University of Michigan, Ann Arbor 48109, USA
    Proteins . 1999
    ....
  7. ncbi 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. ncbi 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 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. AVAILABILITY: http://opm.phar.umich.edu...
  10. ncbi 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
    ....
  11. ncbi 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...