Membrane proteins: Difference between revisions
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==Technical Issues== | ==Technical Issues== | ||
===How To Show The Membrane In Proteopedia=== | |||
*[[Jmol/Visualizing membrane position|Representing membranes in Jmol/Proteopedia]] | *[[Jmol/Visualizing membrane position|Representing membranes in Jmol/Proteopedia]] | ||
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==External Resources== | ==External Resources== | ||
<ref group="xtra">PMID: 33744283</ref><references group="xtra"/> | |||
*[http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html Membrane Proteins of Known 3D Structure] (from the Stephen White laboratory at Univ. California, Irvine, USA). | *[http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html Membrane Proteins of Known 3D Structure] (from the Stephen White laboratory at Univ. California, Irvine, USA). | ||
*[http://www.mpibp-frankfurt.mpg.de/michel/public/memprotstruct.html Membrane Proteins of Known Structure] (from Max Planck Institute in Frankfurt, Germany) not updated since 2006 but useful for tabulation of crystallization conditions. | *[http://www.mpibp-frankfurt.mpg.de/michel/public/memprotstruct.html Membrane Proteins of Known Structure] (from Max Planck Institute in Frankfurt, Germany) not updated since 2006 but useful for tabulation of crystallization conditions. | ||
*[http://opm.phar.umich.edu/ Orientations of Proteins in Membranes (OPM) database] (University of Michigan, USA) features calculated membrane boundaries for all membrane proteins in the PDB. | *[http://opm.phar.umich.edu/ Orientations of Proteins in Membranes (OPM) database] (University of Michigan, USA) features calculated membrane boundaries for all membrane proteins in the PDB. | ||
* [http://memprotmd.bioch.ox.ac.uk/ MemProtMD - A database of membrane proteins embedded in lipid bilayers] features a database of over 5000 intrinsic membrane protein structures identified in the Protein Data Bank, inserted into simulated lipid bilayers using Coarse-Grained Self Assembly Molecular Dynamics simulations. A few of the MemProtMD workflows have been put together as a set of Google Colab notebooks for establishing membrane protein structures in bilayers, see [https://github.com/pstansfeld/MemProtMD/ here]. | |||
* [http://bioinf.cs.ucl.ac.uk/psipred/ The PSIPRED Protein Structure Prediction Server] has a highly accurate method for protein secondary structure prediction for proteins without an empirically-determined 3D structure and features also a widely used transmembrane topology prediction method where the output includes a Kyte-Doolittle Hydropathy Plot. | * [http://bioinf.cs.ucl.ac.uk/psipred/ The PSIPRED Protein Structure Prediction Server] has a highly accurate method for protein secondary structure prediction for proteins without an empirically-determined 3D structure and features also a widely used transmembrane topology prediction method where the output includes a Kyte-Doolittle Hydropathy Plot. | ||
<ref group="xtra">PMID: 17139331</ref><references group="xtra"/> | <ref group="xtra">PMID: 17139331</ref><references group="xtra"/> | ||
