Search Results - "Lomize, Andrei L."

Spatial arrangement of proteins in planar and curved membranes by PPM 3.0 by Lomize, Andrei L., Todd, Spencer C., Pogozheva, Irina D.

“…Cellular protrusions, invaginations, and many intracellular organelles have strongly curved membrane regions. Transmembrane and peripheral membrane proteins…”
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OPM database and PPM web server: resources for positioning of proteins in membranes by Lomize, Mikhail A., Pogozheva, Irina D., Joo, Hyeon, Mosberg, Henry I., Lomize, Andrei L.

“…The Orientations of Proteins in Membranes (OPM) database is a curated web resource that provides spatial positions of membrane-bound peptides and proteins of…”
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Physics-Based Method for Modeling Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules by Lomize, Andrei L, Pogozheva, Irina D

“…Assessment of permeability is a critical step in the drug development process for selection of drug candidates with favorable ADME properties. We have…”
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PerMM: A Web Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules by Lomize, Andrei L, Hage, Jacob M, Schnitzer, Kevin, Golobokov, Konstantin, LaFaive, Mitchell B, Forsyth, Alexander C, Pogozheva, Irina D

“…The PerMM web server and database were developed for quantitative analysis and visualization of passive translocation of bioactive molecules across lipid…”
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OPM: Orientations of Proteins in Membranes database by Lomize, Mikhail A., Lomize, Andrei L., Pogozheva, Irina D., Mosberg, Henry I.

“…The Orientations of Proteins in Membranes (OPM) database provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank…”
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Anisotropic Solvent Model of the Lipid Bilayer. 2. Energetics of Insertion of Small Molecules, Peptides, and Proteins in Membranes by Lomize, Andrei L, Pogozheva, Irina D, Mosberg, Henry I

“…A new computational approach to calculating binding energies and spatial positions of small molecules, peptides, and proteins in the lipid bilayer has been…”
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Positioning of proteins in membranes: A computational approach by Lomize, Andrei L., Pogozheva, Irina D., Lomize, Mikhail A., Mosberg, Henry I.

“…A new computational approach has been developed to determine the spatial arrangement of proteins in membranes by minimizing their transfer energies from water…”
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Antimicrobial action of the cyclic peptide bactenecin on Burkholderia pseudomallei correlates with efficient membrane permeabilization by Madhongsa, Kanjana, Pasan, Supaluk, Phophetleb, Onanong, Nasompag, Sawinee, Thammasirirak, Sompong, Daduang, Sakda, Taweechaisupapong, Suwimol, Lomize, Andrei L, Patramanon, Rina

“…Burkholderia pseudomallei is a category B agent that causes Melioidosis, an acute and chronic disease with septicemia. The current treatment regimen is a heavy…”
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The role of hydrophobic interactions in positioning of peripheral proteins in membranes by Lomize, Andrei L, Pogozheva, Irina D, Lomize, Mikhail A, Mosberg, Henry I

“…Three-dimensional (3D) structures of numerous peripheral membrane proteins have been determined. Biological activity, stability, and conformations of these…”
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TMDOCK: An Energy-Based Method for Modeling α-Helical Dimers in Membranes by Lomize, Andrei L., Pogozheva, Irina D.

“…TMDOCK is a novel computational method for the modeling of parallel homodimers formed by transmembrane (TM) α-helices. Three-dimensional (3D) models of dimers…”
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Membranome: a database for proteome-wide analysis of single-pass membrane proteins by Lomize, Andrei L, Lomize, Mikhail A, Krolicki, Shean R, Pogozheva, Irina D

“…The Membranome database was developed to assist analysis and computational modeling of single-pass (bitopic) transmembrane (TM) proteins and their complexes by…”
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Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers by Lomize, Andrei L, Hage, Jacob M, Pogozheva, Irina D

“…Abstract Motivation Structural studies of TM domains of single-spanning (bitopic) membrane proteins are impeded by their instability, flexibility and…”
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Evolution and adaptation of single-pass transmembrane proteins by Pogozheva, Irina D., Lomize, Andrei L.

“…A comparative analysis of 6039 single-pass (bitopic) membrane proteins from six evolutionarily distant organisms was performed based on data from the…”
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Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer by Pogozheva, Irina D., Cherepanov, Stanislav, Park, Sang-Jun, Raghavan, Malini, Im, Wonpil, Lomize, Andrei L.

“…Homodimeric class 1 cytokine receptors include the erythropoietin (EPOR), thrombopoietin (TPOR), granulocyte colony-stimulating factor 3 (CSF3R), growth…”
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Membranome 3.0: Database of single‐pass membrane proteins with AlphaFold models by Lomize, Andrei L., Schnitzer, Kevin A., Todd, Spencer C., Cherepanov, Stanislav, Outeiral, Carlos, Deane, Charlotte M., Pogozheva, Irina D.

“…The Membranome database provides comprehensive structural information on single‐pass (i.e., bitopic) membrane proteins from six evolutionarily distant…”
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OPRLM: Orientations of proteins in realistic lipid membranes by Park, Sang-Jun, Todd, Spencer C., Pogozheva, Irina D., Lomize, Andrei L., Im, Wonpil

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TMPfold: A Web Tool for Predicting Stability of Transmembrane α-Helix Association by Lomize, Andrei L., Schnitzer, Kevin A., Pogozheva, Irina D.

“…Estimating energies of transmembrane (TM) α-helix association is essential for understanding folding of membrane proteins and formation of their functional…”
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Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes by Pogozheva, Irina D, Armstrong, Grant A, Kong, Lingyang, Hartnagel, Timothy J, Carpino, Carly A, Gee, Stephen E, Picarello, Danielle M, Rubin, Amanda S, Lee, Jumin, Park, Soohyung, Lomize, Andrei L, Im, Wonpil

“…We present a comparative all-atom molecular dynamics simulation study of 18 biomembrane systems with lipid compositions corresponding to eukaryotic, bacterial,…”
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Thermodynamics-Based Molecular Modeling of α‑Helices in Membranes and Micelles by Lomize, Andrei L, Schnitzer, Kevin A, Todd, Spencer C, Pogozheva, Irina D

“…The Folding of Membrane-Associated Peptides (FMAP) method was developed for modeling α-helix formation by linear peptides in micelles and lipid bilayers. FMAP…”
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Structural adaptations of proteins to different biological membranes by Pogozheva, Irina D., Tristram-Nagle, Stephanie, Mosberg, Henry I., Lomize, Andrei L.

“…To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of…”
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