Jmol/Visualizing membrane position
From Proteopedia
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<scene name='78/784276/Opm2/7'>When we apply</scene> a <font color="#909090"><b>hydrophobic</b></font> vs. <font color="magenta"><b>polar</b></font> color scheme, the protein within the lipid bilayer is seen to have a largely hydrophobic surface. The example used here is [[5lil]]. | <scene name='78/784276/Opm2/7'>When we apply</scene> a <font color="#909090"><b>hydrophobic</b></font> vs. <font color="magenta"><b>polar</b></font> color scheme, the protein within the lipid bilayer is seen to have a largely hydrophobic surface. The example used here is [[5lil]]. | ||
| - | ==Methods== | + | ==Methods: Pseudoatoms== |
| - | + | Any protein structure that includes an integral membrane domain can have pseudoatoms added to the [[PDB file]] by the [http://opm.phar.umich.edu/ Orientations of Proteins in Membranes Server]<ref name="opm">PMID: 21890895</ref>. | |
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 19:02, 30 March 2018
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References
- ↑ Files with pseudoatoms can be obtained from the Orientations of Proteins in Membranes Server.
- ↑ 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. 2012 Jan;40(Database issue):D370-6. doi: 10.1093/nar/gkr703., Epub 2011 Sep 2. PMID:21890895 doi:http://dx.doi.org/10.1093/nar/gkr703
