Publications

Lomize AL, Hage JM, Pogozheva ID. Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers. Bioinformatics, 34(6): 1061-1062 (2018) [PubMed]

Pogozheva ID, Lomize AL. Evolution and adaptation of single-pass transmembrane proteins. Biochim Biophys Acta-Biomembranes, 1860(2): 364-377 (2018) [PubMed]

Lomize AL, Pogozheva ID. TMDOCK: An energy-based method for modeling α-helical dimers in membranes. J Mol Biol, 429(3): 390-398 (2016) [PubMed]

Lomize AL, Lomize MA, Krolicki SR, Pogozheva ID. Membranome: a database for proteome-wide analysis of single-pass membrane proteins. Nucleic Acids Res, 45(D1): D250-D255 (2016) [PubMed]

Pogozheva ID, Mosberg HI, Lomize AL. Life at the border: Adaptation of proteins to anisotropic membrane environment. Protein Sci, 23(9): 1165-1196 (2014) [PubMed]

Lomize AL, Pogozheva ID. Solvation models and computational prediction of orientations of peptides and proteins in membranes. Methods Mol Biol, 1063: 125-142 (2013) [PubMed]

Pogozheva ID, Tristram-Nagle S, Mosberg HI, Lomize AL. Structural adaptations of proteins to different biological membranes. Biochim Biophys Acta-Biomembranes, 1828: 2592-2608 (2013) [PubMed]

Lomize MA, Pogozheva ID, Joo H, Mosberg HI, Lomize AL. OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res, 40(Database issue): D370-D376 (2012) [PubMed]

Lomize AL, Pogozheva ID, Mosberg HI. Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects. J Chem Inf Model, 51: 918-929 (2011) [PubMed]

Lomize AL, Pogozheva ID, Mosberg HI. Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes. J Chem Inf Model, 51: 930-946 (2011) [PubMed]

Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI. OPM: orientations of proteins in membranes database. Bioinformatics, 22: 623-625 (2006) [PubMed]

Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI. Positioning of proteins in membranes: a computational approach. Protein Sci, 15: 1318-1333 (2006) [PubMed]

Lomize AL, Pogozheva ID, Mosberg HI. Quantification of helix-helix binding affinities in micelles and lipid bilayers. Protein Sci, 13: 2600-2612 (2004) [PubMed]

Lomize AL, Reibarkh MY, Pogozheva ID. Interatomic potentials and solvation parameters from protein engineering data for buried residues. Protein Sci, 11: 1984-2000 (2002) [PubMed]

Lomize AL, Pogozheva ID, Mosberg HI. Structural organization of G-protein-coupled receptors.
J Comput Aided Mol Des, 13: 325-353 (1999) [PubMed]

Lomize AL, Pogozheva ID, Mosberg HI. Prediction of protein structure: The problem of fold multiplicity. Proteins, 37: 199-203 (1999) [PubMed]

Pogozheva ID, Lomize AL, Mosberg HI. Opioid receptor three-dimensional structures from distance geometry calculations with hydrogen bonding constraints. Biophys J, 75: 612-634 (1998) [PubMed]

Pogozheva ID, Lomize AL, Mosberg HI. The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints. Biophys J, 72: 1963-1985 (1997) [PubMed]

Lomize AL, Mosberg HI. Thermodynamic model of secondary structure for alpha-helical peptides and proteins. Biopolymers, 42: 239-269 (1997) [PubMed]