Orientations of Proteins in Membranes database (Japanese Wikipedia)

Analysis of information sources in references of the Wikipedia article "Orientations of Proteins in Membranes database" in Japanese language version.

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Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio (2007). “TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes”. Biophys. J. 92 (2): 473–481. Bibcode: 2007BpJ....92..473M. doi:10.1529/biophysj.106.092775. PMC 1751395. PMID 17056731.

doi.org

Lomize, Mikhail A.; Lomize, Andrei L; Pogozheva, Irina D.; Mosberg, Henry I. (2006). “OPM: Orientations of Proteins in Membranes database”. Bioinformatics 22 (5): 623–625. doi:10.1093/bioinformatics/btk023. PMID 16397007. http://opm.phar.umich.edu/OPM.pdf.
Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2006). “Positioning of proteins in membranes: A computational approach”. Protein Science 15 (6): 1318–1333. doi:10.1110/ps.062126106. PMC 2242528. PMID 16731967. http://opm.phar.umich.edu/PPM.pdf.
Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2007). “The role of hydrophobic interactions in positioning of peripheral proteins in membranes”. BMC Structural Biology 7 (44): 44. doi:10.1186/1472-6807-7-44. PMC 1934363. PMID 17603894. http://opm.phar.umich.edu/PSALM.pdf.
Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). “Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects”. Journal of Chemical Information and Modeling 51 (4): 918–929. doi:10.1021/ci2000192. PMC 3089899. PMID 21438609.
Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). “Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes”. Journal of Chemical Information and Modeling 51 (4): 930–946. doi:10.1021/ci200020k. PMC 3091260. PMID 21438606.
Malmberg, Nathan J.; Falke, Joseph J. (2005). “Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains”. Annu Rev Biophys Biomol Struct 34: 71–90. doi:10.1146/annurev.biophys.34.040204.144534. PMC 3637887. PMID 15869384.
Spencer, Andrew G.; Thuresson, Elizabeth; Otto, James C.; Song, Inseok; Smith, Tim; DeWitt, David L.; Garavito, R. Michael; Smith, William L. (1999). “The membrane binding domains of prostaglandin endoperoxide H synthases 1 and 2. Peptide mapping and mutational analysis”. J Biol Chem 274 (46): 32936–32942. doi:10.1074/jbc.274.46.32936. PMID 10551860.
Lathrop, Brian; Gadd, Martha; Biltonen, Rodney L.; Rule, Gordon S. (2001). “Changes in Ca²⁺ affinity upon activation of Agkistrodon piscivorus piscivorus phospholipase A₂”. Biochemistry 40 (11): 3264–3272. doi:10.1021/bi001901n. PMID 11258945.
Kutateladze, Tatiana; Overduin, Michael (2001). “Structural Mechanism of Endosome Docking by the FYVE Domain”. Science 291 (5509): 1793–1796. Bibcode: 2001Sci...291.1793K. doi:10.1126/science.291.5509.1793. PMID 11230696.
Tatulian, Suren A.; Qin, Shan; Pande, Abhay H.; He, Xiaomei (2005). “Positioning membrane proteins by novel protein engineering and biophysical approaches”. J Mol Biol 351 (5): 939–947. doi:10.1016/j.jmb.2005.06.080. PMID 16055150. https://zenodo.org/record/894918.
Hristova, Kalina; Wimley, William C.; Mishra, Vinod K.; Anantharamiah, G.M.; Segrest, Jere P.; White, Stephen H. (2 July 1999). “An amphipathic α-helix at a membrane interface: a structural study using a novel X-ray diffraction method”. J Mol Biol 290 (1): 99–117. doi:10.1006/jmbi.1999.2840. PMID 10388560.
Park, Yungki; Helms, Volkhard (2007). “On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins”. Bioinformatics 23 (6): 701–708. doi:10.1093/bioinformatics/btl653. PMID 17237049.
Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio (2007). “TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes”. Biophys. J. 92 (2): 473–481. Bibcode: 2007BpJ....92..473M. doi:10.1529/biophysj.106.092775. PMC 1751395. PMID 17056731.
Punta, Marco; Forrest, Lucy R.; Bigelow, Henry; Kernytsky, Andrew; Liu, Jinfeng; Rost, Burkhard (2007). “Membrane protein prediction methods”. Methods 41 (4): 460–474. doi:10.1016/j.ymeth.2006.07.026. PMC 1934899. PMID 17367718.
Cherezov, V; Yamashita, E; Liu, W; Zhalnina, M; Cramer, WA; Caffrey, M (8 December 2006). “In Meso Structure of the Cobalamin Transporter, BtuB, at 1.95 Ångstrom Resolution”. J. Mol. Biol. 364 (4): 716–734. doi:10.1016/j.jmb.2006.09.022. PMC 1808586. PMID 17028020.
Páli, Tibor; Bashtovyy, Denys; Marsh, Derek (2006). “Stoichiometry of lipid interactions with transmembrane proteins - Deduced from the 3D structures”. Protein Sci. 15 (5): 1153–1161. doi:10.1110/ps.052021406. PMC 2242517. PMID 16641489.

enzim.hu

pdbtm.enzim.hu

PDBTM: Protein Data Bank of Transmembrane Proteins

harvard.edu

ui.adsabs.harvard.edu

Kutateladze, Tatiana; Overduin, Michael (2001). “Structural Mechanism of Endosome Docking by the FYVE Domain”. Science 291 (5509): 1793–1796. Bibcode: 2001Sci...291.1793K. doi:10.1126/science.291.5509.1793. PMID 11230696.
Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio (2007). “TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes”. Biophys. J. 92 (2): 473–481. Bibcode: 2007BpJ....92..473M. doi:10.1529/biophysj.106.092775. PMC 1751395. PMID 17056731.

nih.gov

pubmed.ncbi.nlm.nih.gov

Lomize, Mikhail A.; Lomize, Andrei L; Pogozheva, Irina D.; Mosberg, Henry I. (2006). “OPM: Orientations of Proteins in Membranes database”. Bioinformatics 22 (5): 623–625. doi:10.1093/bioinformatics/btk023. PMID 16397007. http://opm.phar.umich.edu/OPM.pdf.
Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2006). “Positioning of proteins in membranes: A computational approach”. Protein Science 15 (6): 1318–1333. doi:10.1110/ps.062126106. PMC 2242528. PMID 16731967. http://opm.phar.umich.edu/PPM.pdf.
Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2007). “The role of hydrophobic interactions in positioning of peripheral proteins in membranes”. BMC Structural Biology 7 (44): 44. doi:10.1186/1472-6807-7-44. PMC 1934363. PMID 17603894. http://opm.phar.umich.edu/PSALM.pdf.
Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). “Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects”. Journal of Chemical Information and Modeling 51 (4): 918–929. doi:10.1021/ci2000192. PMC 3089899. PMID 21438609.
Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). “Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes”. Journal of Chemical Information and Modeling 51 (4): 930–946. doi:10.1021/ci200020k. PMC 3091260. PMID 21438606.
Malmberg, Nathan J.; Falke, Joseph J. (2005). “Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains”. Annu Rev Biophys Biomol Struct 34: 71–90. doi:10.1146/annurev.biophys.34.040204.144534. PMC 3637887. PMID 15869384.
Spencer, Andrew G.; Thuresson, Elizabeth; Otto, James C.; Song, Inseok; Smith, Tim; DeWitt, David L.; Garavito, R. Michael; Smith, William L. (1999). “The membrane binding domains of prostaglandin endoperoxide H synthases 1 and 2. Peptide mapping and mutational analysis”. J Biol Chem 274 (46): 32936–32942. doi:10.1074/jbc.274.46.32936. PMID 10551860.
Lathrop, Brian; Gadd, Martha; Biltonen, Rodney L.; Rule, Gordon S. (2001). “Changes in Ca²⁺ affinity upon activation of Agkistrodon piscivorus piscivorus phospholipase A₂”. Biochemistry 40 (11): 3264–3272. doi:10.1021/bi001901n. PMID 11258945.
Kutateladze, Tatiana; Overduin, Michael (2001). “Structural Mechanism of Endosome Docking by the FYVE Domain”. Science 291 (5509): 1793–1796. Bibcode: 2001Sci...291.1793K. doi:10.1126/science.291.5509.1793. PMID 11230696.
Tatulian, Suren A.; Qin, Shan; Pande, Abhay H.; He, Xiaomei (2005). “Positioning membrane proteins by novel protein engineering and biophysical approaches”. J Mol Biol 351 (5): 939–947. doi:10.1016/j.jmb.2005.06.080. PMID 16055150. https://zenodo.org/record/894918.
Hristova, Kalina; Wimley, William C.; Mishra, Vinod K.; Anantharamiah, G.M.; Segrest, Jere P.; White, Stephen H. (2 July 1999). “An amphipathic α-helix at a membrane interface: a structural study using a novel X-ray diffraction method”. J Mol Biol 290 (1): 99–117. doi:10.1006/jmbi.1999.2840. PMID 10388560.
Park, Yungki; Helms, Volkhard (2007). “On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins”. Bioinformatics 23 (6): 701–708. doi:10.1093/bioinformatics/btl653. PMID 17237049.
Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio (2007). “TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes”. Biophys. J. 92 (2): 473–481. Bibcode: 2007BpJ....92..473M. doi:10.1529/biophysj.106.092775. PMC 1751395. PMID 17056731.
Punta, Marco; Forrest, Lucy R.; Bigelow, Henry; Kernytsky, Andrew; Liu, Jinfeng; Rost, Burkhard (2007). “Membrane protein prediction methods”. Methods 41 (4): 460–474. doi:10.1016/j.ymeth.2006.07.026. PMC 1934899. PMID 17367718.
Cherezov, V; Yamashita, E; Liu, W; Zhalnina, M; Cramer, WA; Caffrey, M (8 December 2006). “In Meso Structure of the Cobalamin Transporter, BtuB, at 1.95 Ångstrom Resolution”. J. Mol. Biol. 364 (4): 716–734. doi:10.1016/j.jmb.2006.09.022. PMC 1808586. PMID 17028020.
Páli, Tibor; Bashtovyy, Denys; Marsh, Derek (2006). “Stoichiometry of lipid interactions with transmembrane proteins - Deduced from the 3D structures”. Protein Sci. 15 (5): 1153–1161. doi:10.1110/ps.052021406. PMC 2242517. PMID 16641489.

pmc.ncbi.nlm.nih.gov

Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2006). “Positioning of proteins in membranes: A computational approach”. Protein Science 15 (6): 1318–1333. doi:10.1110/ps.062126106. PMC 2242528. PMID 16731967. http://opm.phar.umich.edu/PPM.pdf.
Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2007). “The role of hydrophobic interactions in positioning of peripheral proteins in membranes”. BMC Structural Biology 7 (44): 44. doi:10.1186/1472-6807-7-44. PMC 1934363. PMID 17603894. http://opm.phar.umich.edu/PSALM.pdf.
Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). “Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects”. Journal of Chemical Information and Modeling 51 (4): 918–929. doi:10.1021/ci2000192. PMC 3089899. PMID 21438609.
Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). “Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes”. Journal of Chemical Information and Modeling 51 (4): 930–946. doi:10.1021/ci200020k. PMC 3091260. PMID 21438606.
Malmberg, Nathan J.; Falke, Joseph J. (2005). “Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains”. Annu Rev Biophys Biomol Struct 34: 71–90. doi:10.1146/annurev.biophys.34.040204.144534. PMC 3637887. PMID 15869384.
Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio (2007). “TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes”. Biophys. J. 92 (2): 473–481. Bibcode: 2007BpJ....92..473M. doi:10.1529/biophysj.106.092775. PMC 1751395. PMID 17056731.
Punta, Marco; Forrest, Lucy R.; Bigelow, Henry; Kernytsky, Andrew; Liu, Jinfeng; Rost, Burkhard (2007). “Membrane protein prediction methods”. Methods 41 (4): 460–474. doi:10.1016/j.ymeth.2006.07.026. PMC 1934899. PMID 17367718.
Cherezov, V; Yamashita, E; Liu, W; Zhalnina, M; Cramer, WA; Caffrey, M (8 December 2006). “In Meso Structure of the Cobalamin Transporter, BtuB, at 1.95 Ångstrom Resolution”. J. Mol. Biol. 364 (4): 716–734. doi:10.1016/j.jmb.2006.09.022. PMC 1808586. PMID 17028020.
Páli, Tibor; Bashtovyy, Denys; Marsh, Derek (2006). “Stoichiometry of lipid interactions with transmembrane proteins - Deduced from the 3D structures”. Protein Sci. 15 (5): 1153–1161. doi:10.1110/ps.052021406. PMC 2242517. PMID 16641489.

ncbi.nlm.nih.gov

Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). “Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects”. Journal of Chemical Information and Modeling 51 (4): 918–929. doi:10.1021/ci2000192. PMC 3089899. PMID 21438609.
Lomize, AL; Pogozheva, ID; Mosberg, HI (2011). “Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes”. Journal of Chemical Information and Modeling 51 (4): 930–946. doi:10.1021/ci200020k. PMC 3091260. PMID 21438606.
Malmberg, Nathan J.; Falke, Joseph J. (2005). “Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains”. Annu Rev Biophys Biomol Struct 34: 71–90. doi:10.1146/annurev.biophys.34.040204.144534. PMC 3637887. PMID 15869384.
Punta, Marco; Forrest, Lucy R.; Bigelow, Henry; Kernytsky, Andrew; Liu, Jinfeng; Rost, Burkhard (2007). “Membrane protein prediction methods”. Methods 41 (4): 460–474. doi:10.1016/j.ymeth.2006.07.026. PMC 1934899. PMID 17367718.
Cherezov, V; Yamashita, E; Liu, W; Zhalnina, M; Cramer, WA; Caffrey, M (8 December 2006). “In Meso Structure of the Cobalamin Transporter, BtuB, at 1.95 Ångstrom Resolution”. J. Mol. Biol. 364 (4): 716–734. doi:10.1016/j.jmb.2006.09.022. PMC 1808586. PMID 17028020.
Páli, Tibor; Bashtovyy, Denys; Marsh, Derek (2006). “Stoichiometry of lipid interactions with transmembrane proteins - Deduced from the 3D structures”. Protein Sci. 15 (5): 1153–1161. doi:10.1110/ps.052021406. PMC 2242517. PMID 16641489.

sciencemag.org

stke.sciencemag.org

ST NetWatch: Protein Databases review of OPM in Signal Transduction NetWatch list from Science

semanticscholar.org

Hristova, Kalina; Wimley, William C.; Mishra, Vinod K.; Anantharamiah, G.M.; Segrest, Jere P.; White, Stephen H. (2 July 1999). “An amphipathic α-helix at a membrane interface: a structural study using a novel X-ray diffraction method”. J Mol Biol 290 (1): 99–117. doi:10.1006/jmbi.1999.2840. PMID 10388560.

umich.edu

opm.phar.umich.edu

Lomize, Mikhail A.; Lomize, Andrei L; Pogozheva, Irina D.; Mosberg, Henry I. (2006). “OPM: Orientations of Proteins in Membranes database”. Bioinformatics 22 (5): 623–625. doi:10.1093/bioinformatics/btk023. PMID 16397007. http://opm.phar.umich.edu/OPM.pdf.
Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2006). “Positioning of proteins in membranes: A computational approach”. Protein Science 15 (6): 1318–1333. doi:10.1110/ps.062126106. PMC 2242528. PMID 16731967. http://opm.phar.umich.edu/PPM.pdf.
Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2007). “The role of hydrophobic interactions in positioning of peripheral proteins in membranes”. BMC Structural Biology 7 (44): 44. doi:10.1186/1472-6807-7-44. PMC 1934363. PMID 17603894. http://opm.phar.umich.edu/PSALM.pdf.

zenodo.org

Tatulian, Suren A.; Qin, Shan; Pande, Abhay H.; He, Xiaomei (2005). “Positioning membrane proteins by novel protein engineering and biophysical approaches”. J Mol Biol 351 (5): 939–947. doi:10.1016/j.jmb.2005.06.080. PMID 16055150. https://zenodo.org/record/894918.