User:Eric Martz/Introduction to Structural Bioinformatics 2016 - Revision history

Eric Martz at 00:15, 28 March 2016

2016-03-28T00:15:05Z

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	10: Be sure to say what kind of bond you are describing, for example "hydrogen bond".		10: Be sure to say what kind of bond you are describing, for example "hydrogen bond".

			Show them where the link to the abstract is. Ask them to read it an use information learned there in their reports.

	Insist that they do their own consurf jobs. The patterns in Ppda consurfDB are not very believable. Probably too many protein functions included.		Insist that they do their own consurf jobs. The patterns in Ppda consurfDB are not very believable. Probably too many protein functions included.

2016-03-27T23:55:20Z

← Older revision		Revision as of 23:55, 27 March 2016
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	10: Be sure to say what kind of bond you are describing, for example "hydrogen bond".		10: Be sure to say what kind of bond you are describing, for example "hydrogen bond".

			Insist that they do their own consurf jobs. The patterns in Ppda consurfDB are not very believable. Probably too many protein functions included.

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2016-03-27T18:02:33Z

← Older revision		Revision as of 18:02, 27 March 2016
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	2: chains in the asymmetric unit to be clear. And suggest cartoon so each chain has a different color.		2: chains in the asymmetric unit to be clear. And suggest cartoon so each chain has a different color.

			10: Be sure to say what kind of bond you are describing, for example "hydrogen bond".

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2016-03-26T19:26:12Z

← Older revision		Revision as of 19:26, 26 March 2016
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	<!-- NOTES ~~FOR~~ 2016:		<!-- NOTES FROM 2016:
			For 2017:
			Some people had no catpi so give them an alternative.
			2: chains in the asymmetric unit to be clear. And suggest cartoon so each chain has a different color.



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	Section 2: "1-3 character"		Section 2: "1-3 character"

2016-02-25T18:31:18Z

Section 10 - Contacts/Non-covalent Bonds

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	===Section 10 - Contacts/Non-covalent Bonds===		===Section 10 - Contacts/Non-covalent Bonds===
			Example: [http://firstglance.jmol.org/fg.htm?mol=4d7b 4d7b].
	#Click ''Contacts'' in the ''Tools Tab'' in FirstGlance.		#Click ''Contacts'' in the ''Tools Tab'' in FirstGlance.
	#Change target selection to ''Residues/Groups''.		#Change target selection to ''Residues/Groups''.

2016-02-23T19:35:57Z

VI. Report Slides

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	*Additional work beyond the minimum required may earn extra credit.		*Additional work beyond the minimum required may earn extra credit.

	*<font color="red">Due date: midnight Thursday ~~May~~ 3.</font>		*<font color="red">Due date: midnight Thursday March 3.</font>

	<font color='e000e0'>This is not a test. It is to help you learn by doing. Ask for help!</font>		<font color='e000e0'>This is not a test. It is to help you learn by doing. Ask for help!</font>

2016-02-23T19:03:20Z

VI. Report Slides

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	*Additional work beyond the minimum required may earn extra credit.		*Additional work beyond the minimum required may earn extra credit.

			*<font color="red">Due date: midnight Thursday May 3.</font>

	<font color='e000e0'>This is not a test. It is to help you learn by doing. Ask for help!</font>		<font color='e000e0'>This is not a test. It is to help you learn by doing. Ask for help!</font>

2016-02-23T17:12:13Z

Section 3: Evolutionary Conservation

← Older revision		Revision as of 17:12, 23 February 2016
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	===Section 3: Evolutionary Conservation===		===Section 3: Evolutionary Conservation===
	See [[Introduction to Evolutionary Conservation]].   (Example 4d7b: [http://consurf.tau.ac.il/results/1454623073/output_with_form.php ConSurf], [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/pdb/4d7b_consurf1454623073_pipe.pdb Result])		See [[Introduction to Evolutionary Conservation]].   (Example 4d7b: [http://consurf.tau.ac.il/results/1454623073/output_with_form.php ConSurf], [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/atlas/pdb/4d7b_consurf1454623073_pipe.pdb Result])

	Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show <font color='e000e0'><b>two snapshots</b></font> illustrating a highly conserved region, and a contrasting region.		Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show <font color='e000e0'><b>two snapshots</b></font> illustrating a highly conserved region, and a contrasting region.

2016-02-18T17:29:04Z

IV. Choose a Molecule to Explore

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	**X-ray results should have resolution of 3 Å or better.		**X-ray results should have resolution of 3 Å or better.
	*Here are some ways to find a protein with known structure:		*Here are some ways to find a protein with known structure:
	# '''Recommended:''' Atlas of Macromolecules ([http://atlas.molviz.org Atlas.MolviZ.Org]). Choose a "Straightforward" or "Challenging" (not "Enormous") molecule that has protein and ligand.		# '''Recommended:''' <span style="font-size:150%;">Atlas of Macromolecules ([http://atlas.molviz.org Atlas.MolviZ.Org]).</span> Choose a "Straightforward" or "Challenging" (not "Enormous") molecule that has protein and ligand.
	# [http://pdb101.rcsb.org/motm/motm-by-category Molecule of the Month] at the PDB. Look for PDB codes in the article, and use [http://firstglance.jmol.org FirstGlance] to view them.		# [http://pdb101.rcsb.org/motm/motm-by-category Molecule of the Month] at the PDB. Look for PDB codes in the article, and use [http://firstglance.jmol.org FirstGlance] to view them.
	# [http://proteopedia.org/wiki/index.php/Topic_pages Topic Pages] in Proteopedia, or its [http://proteopedia.org/wiki/index.php/Table_of_Contents Table of Contents].		# [http://proteopedia.org/wiki/index.php/Topic_pages Topic Pages] in Proteopedia, or its [http://proteopedia.org/wiki/index.php/Table_of_Contents Table of Contents].

2016-02-18T16:49:39Z

Section 3: Evolutionary Conservation

← Older revision		Revision as of 16:49, 18 February 2016
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	===Section 3: Evolutionary Conservation===		===Section 3: Evolutionary Conservation===
	See [[Introduction to Evolutionary Conservation]].   ([http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/pdb/4d7b_consurf1454623073_pipe.pdb ~~4d7b~~])		See [[Introduction to Evolutionary Conservation]].   (Example 4d7b: [http://consurf.tau.ac.il/results/1454623073/output_with_form.php ConSurf], [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/pdb/4d7b_consurf1454623073_pipe.pdb Result])

	Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show <font color='e000e0'><b>two snapshots</b></font> illustrating a highly conserved region, and a contrasting region.		Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show <font color='e000e0'><b>two snapshots</b></font> illustrating a highly conserved region, and a contrasting region.