Membrane proteins - Revision history

Wayne Decatur: add the google Colab notebooks

Wayne Decatur — Thu, 14 Apr 2022 19:32:09 GMT

add the google Colab notebooks

←Older revision		Revision as of 19:32, 14 April 2022
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	*[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.	+	* [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"/>

Wayne Decatur: add MemProtMD

Wayne Decatur — Thu, 14 Apr 2022 19:28:27 GMT

add MemProtMD

←Older revision		Revision as of 19:28, 14 April 2022
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	*[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.
	* [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"/>

Eric Martz: /* External Resources */

Eric Martz — Sat, 28 Aug 2021 18:01:33 GMT

External Resources

←Older revision		Revision as of 18:01, 28 August 2021
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	==External Resources==		==External Resources==
-	*Highlighting membrane protein structure and function: A celebration of the Protein Data Bank (2021)<ref>PMID: 33744283 </ref>.	+	<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.

Eric Martz: /* External Resources */

Eric Martz — Sat, 28 Aug 2021 17:59:43 GMT

External Resources

←Older revision		Revision as of 17:59, 28 August 2021
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	==External Resources==		==External Resources==
		+	*Highlighting membrane protein structure and function: A celebration of the Protein Data Bank (2021)<ref>PMID: 33744283 </ref>.
	*[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.

Alexander Berchansky at 13:11, 1 March 2021

Alexander Berchansky — Mon, 01 Mar 2021 13:11:11 GMT

←Older revision		Revision as of 13:11, 1 March 2021
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	==Proteopedia Articles==		==Proteopedia Articles==
		+	*[[Receptor#Transmembrane (cell surface) receptors]]
	* [[Photosystem II]]		* [[Photosystem II]]
	*Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, [[2ic8]].		*Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, [[2ic8]].

Wayne Decatur at 14:20, 30 March 2018

Wayne Decatur — Fri, 30 Mar 2018 14:20:53 GMT

←Older revision		Revision as of 14:20, 30 March 2018
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	*[[G protein-coupled receptor\|G protein-coupled receptors]]		*[[G protein-coupled receptor\|G protein-coupled receptors]]
	*[[A Physical Model of the β2-Adrenergic Receptor ]]		*[[A Physical Model of the β2-Adrenergic Receptor ]]
		+
		+	==Technical Issues==
		+	*[[Jmol/Visualizing membrane position\|Representing membranes in Jmol/Proteopedia]]

	==See Also==		==See Also==

Nikki Hunter: /* See Also */

Nikki Hunter — Thu, 21 Nov 2013 19:09:04 GMT

Eric Martz: /* Proteopedia Articles */

Eric Martz — Fri, 02 Mar 2012 21:12:35 GMT

Proteopedia Articles

←Older revision		Revision as of 21:12, 2 March 2012
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	==Proteopedia Articles==		==Proteopedia Articles==
		+	* [[Photosystem II]]
	*Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, [[2ic8]].		*Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, [[2ic8]].
	*[[Ion channels]]		*[[Ion channels]]

Wayne Decatur at 02:46, 7 September 2011

Wayne Decatur — Wed, 07 Sep 2011 02:46:21 GMT

←Older revision		Revision as of 02:46, 7 September 2011
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	==Proteopedia Articles==		==Proteopedia Articles==
-	*[[A Physical Model of the β2-Adrenergic Receptor ]]
	*Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, [[2ic8]].		*Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, [[2ic8]].
	*[[Ion channels]]		*[[Ion channels]]
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	*[[Urea transporter]]		*[[Urea transporter]]
	*[[Ionotropic Glutamate Receptor\|Glutamate receptor]]		*[[Ionotropic Glutamate Receptor\|Glutamate receptor]]
-	*[[G protein-coupled receptor\|G protein-coupled receptors]	+	*[[G protein-coupled receptor\|G protein-coupled receptors]]
		+	*[[A Physical Model of the β2-Adrenergic Receptor ]]

	==See Also==		==See Also==

Wayne Decatur at 02:45, 7 September 2011

Wayne Decatur — Wed, 07 Sep 2011 02:45:50 GMT

←Older revision		Revision as of 02:45, 7 September 2011
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	*[[Pore forming toxin, α-hemolysin]]		*[[Pore forming toxin, α-hemolysin]]
	*[[Urea transporter]]		*[[Urea transporter]]
-	*[[Glutamate ~~receptor (GluA2)~~\|~~The~~ Glutamate ~~Receptor (GluA2)~~]]	+	*[[Ionotropic Glutamate Receptor\|Glutamate receptor]]
		+	*[[G protein-coupled receptor\|G protein-coupled receptors]

	==See Also==		==See Also==

←Older revision		Revision as of 19:09, 21 November 2013
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	==See Also==		==See Also==
	* [[Secondary structure]]		* [[Secondary structure]]
		+	* [[Ligand Binding N-Terminal of Metabotropic Glutamate Receptors]]

	==External Resources==		==External Resources==