Baza podataka orijentacija proteina u membranama

Periferni protein iz OPM baze podataka (P40phox PX domen NADPH oksidaze). Srednja ravan lipidnog dvosloja - srne tačke. Granica ugljenovodoničnog centralnog regiona - plave tačke (intracelularna strana). Slog lipidnih fosfata - žute tačke.

Baza podataka orijentacija proteina u membranama (engl. Orientations of Proteins in Membranes, OPM) sadrži prostorne orijentacije proteinskih tri-dimenzionalnih struktura u odnosu na lipidni dvosloj.^[1]^[2]^[3] Ova baza podatak je bila korišćena u eksperimentalnim i teoretskim studijama za membranu-vezanih proteina.^[4]^[5]^[6]^[7]^[8]

^ Lomize, Mikhail A.; Lomize, Andrei L; Pogozheva, Irina D.; Mosberg, Henry I. (2006). „OPM: Orientations of Proteins in Membranes database” (PDF). Bioinformatics. 22 (5): 623—625. PMID 16397007. doi:10.1093/bioinformatics/btk023.
^ Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2006). „Positioning of proteins in membranes: A computational approach” (PDF). Protein Science. 15 (6): 1318—1333. PMC 2242528 . PMID 16731967. doi:10.1110/ps.062126106.
^ 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” (PDF). BMC Structural Biology. 7 (44): 44. PMC 1934363 . PMID 17603894. doi:10.1186/1472-6807-7-44.
^ 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. PMID 17237049. doi:10.1093/bioinformatics/btl653.
^ Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio (2007). „TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes”. Biophysical Journal. 92 (2): 473—481. PMC 1751395 . PMID 17056731. doi:10.1529/biophysj.106.092775.
^ Punta, Marco; Forrest, Lucy R.; Bigelow, Henry; Kernytsky, Andrew; Liu, Jinfeng; Rost, Burkhard (2007). „Membrane protein prediction methods”. Methods. 41 (4): 460—474. PMC 1934899 . PMID 17367718. doi:10.1016/j.ymeth.2006.07.026.
^ Cherezov, V; Yamashita, E; Liu, W; Zhalnina, M; Cramer, WA; Caffrey, M (2006). „In Meso Structure of the Cobalamin Transporter, BtuB, at 1.95 Ångstrom Resolution”. J. Mol. Biol. 364 (4): 716—734. PMC 1808586 . PMID 17028020. doi:10.1016/j.jmb.2006.09.022.
^ 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. PMC 2242517 . PMID 16641489. doi:10.1110/ps.052021406.

[OPM-cite-1] Lomize, Mikhail A.; Lomize, Andrei L; Pogozheva, Irina D.; Mosberg, Henry I. (2006). „OPM: Orientations of Proteins in Membranes database” (PDF). Bioinformatics. 22 (5): 623—625. PMID 16397007. doi:10.1093/bioinformatics/btk023.

[OPM1-2] Lomize, Andrei L; Pogozheva, Irina D.; Lomize, Mikhail A.; Mosberg, Henry I. (2006). „Positioning of proteins in membranes: A computational approach” (PDF). Protein Science. 15 (6): 1318—1333. PMC 2242528 . PMID 16731967. doi:10.1110/ps.062126106.

[peripheral-3] 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” (PDF). BMC Structural Biology. 7 (44): 44. PMC 1934363 . PMID 17603894. doi:10.1186/1472-6807-7-44.

[park-helms-4] 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. PMID 17237049. doi:10.1093/bioinformatics/btl653.

[marsh-jost-peggion-5] Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio (2007). „TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes”. Biophysical Journal. 92 (2): 473—481. PMC 1751395 . PMID 17056731. doi:10.1529/biophysj.106.092775.

[pfb-2007-6] Punta, Marco; Forrest, Lucy R.; Bigelow, Henry; Kernytsky, Andrew; Liu, Jinfeng; Rost, Burkhard (2007). „Membrane protein prediction methods”. Methods. 41 (4): 460—474. PMC 1934899 . PMID 17367718. doi:10.1016/j.ymeth.2006.07.026.

[cyl-2006-7] Cherezov, V; Yamashita, E; Liu, W; Zhalnina, M; Cramer, WA; Caffrey, M (2006). „In Meso Structure of the Cobalamin Transporter, BtuB, at 1.95 Ångstrom Resolution”. J. Mol. Biol. 364 (4): 716—734. PMC 1808586 . PMID 17028020. doi:10.1016/j.jmb.2006.09.022.

[pbm-2006-8] 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. PMC 2242517 . PMID 16641489. doi:10.1110/ps.052021406.

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