Structure prediction of membrane proteins.

Modeling of protein-protein and ligand-protein interactions.

GPCR Modeling

GPCR-G protein complexes

OPM: orientations of proteins in membranes

Opioid receptor-ligand complexes

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

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

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

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)

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)

Lomize AL, Pogozheva ID, Mosberg HI
Development of a model for the delta-opioid receptor pharmacophore: 3. Comparison of the cyclic tetrapeptide, Tyr-c[D-Cys-Phe-D-Pen]OH with other conformationally constrained delta-receptor selective ligands.
Biopolymers., 38: 221-234 (1996)

Pogozheva ID, Lomize AL, Mosberg HI
Modeling of secretin-like G protein coupled receptors
Peptides for the New Millennium, Proceedings of the 16th American Peptide Symposium: 585-586 (2000)

Mosberg HI, Dua RK, Pogozheva ID, Lomize AL
Development of a model for the delta-opioid receptor pharmacophore. 4. Residue 3dehydrophenylalanine analogues of Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13) confirmrequired gauche orientation of aromatic side chain.
Biopolymers, 39: 287-296 (1996)

Fowler CB, Pogozheva ID, LeVine H 3rd, Mosberg HI.
Refinement of a homology model of the mu-opioid receptor using distance constraints from intrinsic and engineered zinc-binding sites.
Biochemistry., 43: 8700-8710 (2004)

Munshi UM, Pogozheva ID, Menon KM
Highly conserved serine in the third transmembrane helix of the luteinizing hormone/human chorionic gonadotropin receptor regulates receptor activation.
Biochemistry., 42: 3708-3715 (2003)

Poulsen A, Bjornholm B, Gundertofte K, Pogozheva ID, Liljefors T
Pharmacophore and receptor models for neurokinin receptors.
J. Comput. Aided. Mol. Des., 17: 765-783 (2003)

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

Fowler CB, Pogozheva ID, Lomize AL, LeVine H, Mosberg HI
Complex of active mu-opioid receptor with cyclic peptide agonist modeled from experimental constraints.
Biochemistry, 43: 15796-15810 (2004)

Chai B-X, Pogozheva ID, Lai Y-M, Li J-Y, Neubig RR, Mosberg HI, Gantz I
Receptor-antagonist interactions in the complexes of agouti protein and agouti-related protein with human melanocortin 1 and 4 receptors.
Biochemistry, 44: 3418-3431 (2005)

Pogozheva ID, Chai B-X, Lomize AL, Fong TM, Weinberg DH, Nargund RH, Mulholland MW, Gantz I, Mosberg HI
Interactions of human melanocortin receptor-4 with small-molecule agonists.
Biochemistry, 44: 11329-11341 (2005)

Przydzial MJ, Pogozheva ID, Bosse KE, Andrews SM, Tod A, Tharp TA, Traynor JR, Mosberg HI
Roles of residues 3 and 4 in cyclic tetrapeptide ligand recognition by the kappa- opioid receptor
J. Pept. Res., 65: 333-342 (2005)

Przydzial MJ, Pogozheva ID, Ho JC, Tharp TA, Drankhan KE, Sawyer E, Traynor JR, Mosberg HI
Design of high affinity cyclic pentapeptide ligands for kappa-opioid receptors.
J. Pept. Res., 66: 255-262 (2005)

Pogozheva ID, Przydzial MJ, Mosberg HI
Homology modeling of opioid receptor-ligand complexes using experimental constraints.
AAPS J., 7: E434-E448 (2005)

Kneen MM, Pogozheva ID, Kenyon GL, McLeish MJ
Exploring the active site of benzaldehyde lyase by modeling and mutagenesis
Biochim. Biophys. Acta, 1753: 263-271 (2005)

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

Proneth B, Xiang Z, Pogozheva ID, Litherland SA, Gorbatyuk OS, Shaw AM, Millard WJ, Mosberg HI, Haskell-Luevano C
Molecular mechanism of the constitutive activation of the L250Q human melanocortin-4 receptor polymorphism
Chem. Biol. Drug. Des., 67: 215-229 (2006)

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