Exercise:Malaria Vaccine - Revision history

Carol: /* Searching UniProt */

2025-10-28T15:28:53Z

Searching UniProt

← Older revision		Revision as of 17:28, 28 October 2025
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	Some of the hits you find in this way are very short (you can try to sort them by length by clicking the <u>Length</u> heading). These short proteins might be fragments.		Some of the hits you find in this way are very short (you can try to sort them by length by clicking the <u>Length</u> heading). These short proteins might be fragments.

	'''2k)''' How many of the hits are complete (not annotated as fragments)?		'''2k)''' How many of the hits are complete (not annotated as fragments)? ('''Tip:''' see question 3.7 in [[Exercise: The protein database UniProt\|the UniProt exercise]]).
	~~<!--~~('''Tip:''' see question 16 in [[Exercise: The protein database UniProt\|the UniProt exercise]]).~~-->~~

	'''2l)''' Do any of these proteins have a determined 3D structure? In other words: Do any proteins from the previous search have a cross-reference to the database PDB? ('''Tip:''' you should look for <u>Cross-references</u> in the menu, and again place a <tt>*</tt> in the field). If yes, what are their names and accession codes?		'''2l)''' Do any of these proteins have a determined 3D structure? In other words: Do any proteins from the previous search have a cross-reference to the database PDB? ('''Tip:''' you should look for <u>Cross-references</u> in the menu, and again place a <tt>*</tt> in the field). If yes, what are their names and accession codes?

Carol: /* Searching UniProt */

2025-10-28T15:24:41Z

Searching UniProt

← Older revision		Revision as of 17:24, 28 October 2025
Line 93:		Line 93:
	Some of the hits you find in this way are very short (you can try to sort them by length by clicking the <u>Length</u> heading). These short proteins might be fragments.		Some of the hits you find in this way are very short (you can try to sort them by length by clicking the <u>Length</u> heading). These short proteins might be fragments.

	'''2k)''' How many of the hits are complete (not annotated as fragments)? ('''Tip:''' see question 16 in [[Exercise: The protein database UniProt\|the UniProt exercise]]).		'''2k)''' How many of the hits are complete (not annotated as fragments)?
			<!--('''Tip:''' see question 16 in [[Exercise: The protein database UniProt\|the UniProt exercise]]).-->

	'''2l)''' Do any of these proteins have a determined 3D structure? In other words: Do any proteins from the previous search have a cross-reference to the database PDB? ('''Tip:''' you should look for <u>Cross-references</u> in the menu, and again place a <tt>*</tt> in the field). If yes, what are their names and accession codes?		'''2l)''' Do any of these proteins have a determined 3D structure? In other words: Do any proteins from the previous search have a cross-reference to the database PDB? ('''Tip:''' you should look for <u>Cross-references</u> in the menu, and again place a <tt>*</tt> in the field). If yes, what are their names and accession codes?

Henni: /* Epitope prediction */

2025-10-28T12:41:29Z

Epitope prediction

← Older revision		Revision as of 14:41, 28 October 2025
Line 195:		Line 195:

	'''Hint:''' If the prediction takes more than 5min to run, you can follow this link to pre-calculated results:		'''Hint:''' If the prediction takes more than 5min to run, you can follow this link to pre-calculated results:
	https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6900B2C30023DC3C6C456FAC&wait=20		https://teaching.healthtech.dtu.dk/material/22111/BepiPred-2.0/
	Please note that this will only work until Wed 29-10-25 at 13hs		<!-- https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6900B2C30023DC3C6C456FAC&wait=20
			Please note that this will only work until Wed 29-10-25 at 13hs -->

	'''Question 4d''': Create a table with the following information about the predicted epitopes:		'''Question 4d''': Create a table with the following information about the predicted epitopes:

Carol: /* Epitope prediction */

2025-10-28T12:18:09Z

Epitope prediction

← Older revision		Revision as of 14:18, 28 October 2025
Line 196:		Line 196:
	'''Hint:''' If the prediction takes more than 5min to run, you can follow this link to pre-calculated results:		'''Hint:''' If the prediction takes more than 5min to run, you can follow this link to pre-calculated results:
	https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6900B2C30023DC3C6C456FAC&wait=20		https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6900B2C30023DC3C6C456FAC&wait=20
			Please note that this will only work until Wed 29-10-25 at 13hs

	'''Question 4d''': Create a table with the following information about the predicted epitopes:		'''Question 4d''': Create a table with the following information about the predicted epitopes:

Carol: /* Prediction of B-cell epitopes in a membrane protein */

2025-10-28T12:12:31Z

Prediction of B-cell epitopes in a membrane protein

← Older revision		Revision as of 14:12, 28 October 2025
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	'''Hint:''' If the prediction takes more than 5min to run, you can follow this link to pre-calculated results:		'''Hint:''' If the prediction takes more than 5min to run, you can follow this link to pre-calculated results:
	https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=~~68FF4033001DB8C00F4738DE~~&wait=20		https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6900B2C30023DC3C6C456FAC&wait=20

	'''Question 4d''': Create a table with the following information about the predicted epitopes:		'''Question 4d''': Create a table with the following information about the predicted epitopes:

Carol: /* Epitope prediction */

2025-10-27T11:16:51Z

Epitope prediction

← Older revision		Revision as of 13:16, 27 October 2025
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	* '''Hint:''' there should be '''6''' such epitopes, and the second one starts at position '''L23'''		* '''Hint:''' there should be '''6''' such epitopes, and the second one starts at position '''L23'''

	[[image:~~BepiPred-2_onIEDB~~.png\|thumb\|center\|600px\|Click to zoom]]		[[image:BepiPred2.png\|thumb\|center\|600px\|Click to zoom]]

	'''Hint:''' If the prediction takes more than 5min to run, you can follow this link to pre-calculated results:		'''Hint:''' If the prediction takes more than 5min to run, you can follow this link to pre-calculated results:

Carol: /* Epitope prediction */

2025-10-27T11:13:36Z

Epitope prediction

← Older revision		Revision as of 13:13, 27 October 2025
Line 193:		Line 193:

	[[image:BepiPred-2_onIEDB.png\|thumb\|center\|600px\|Click to zoom]]		[[image:BepiPred-2_onIEDB.png\|thumb\|center\|600px\|Click to zoom]]

			'''Hint:''' If the prediction takes more than 5min to run, you can follow this link to pre-calculated results:
			https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=68FF4033001DB8C00F4738DE&wait=20

	'''Question 4d''': Create a table with the following information about the predicted epitopes:		'''Question 4d''': Create a table with the following information about the predicted epitopes:

Carol: /* Epitope prediction */

2025-10-27T10:52:12Z

Epitope prediction

← Older revision		Revision as of 12:52, 27 October 2025
Line 187:		Line 187:

	You can now run the '''BepiPred 2.0''' prediction server on the domain sequence (ONLY the subset extracted above). Run it and then adjust the following on the '''results page''':		You can now run the '''BepiPred 2.0''' prediction server on the domain sequence (ONLY the subset extracted above). Run it and then adjust the following on the '''results page''':
	* Set '''threshold''' to '''0.55'''		* Set '''threshold''' to '''0.53'''
	This gives us a reasonable amount of epitopes to continue our work with:		This gives us a reasonable amount of epitopes to continue our work with:
	* Write down the start/end sequence positions of all epitopes of at least '''8 amino acids'''		* Write down the start/end sequence positions of all epitopes of at least '''5 amino acids'''
	* '''Hint:''' there should be '''7''' such epitopes, and the ~~last~~ one starts at position '''~~276~~'''		* '''Hint:''' there should be '''6''' such epitopes, and the second one starts at position '''L23'''

	[[image:BepiPred-2_onIEDB.png\|thumb\|center\|600px\|Click to zoom]]		[[image:BepiPred-2_onIEDB.png\|thumb\|center\|600px\|Click to zoom]]

Carol: /* Epitope prediction */

2025-10-27T10:47:20Z

Epitope prediction

← Older revision		Revision as of 12:47, 27 October 2025
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	For predicting which parts of the protein are potential epitopes, we'll use the '''BepiPred 2.0 server''', which was created here at DTU.		For predicting which parts of the protein are potential epitopes, we'll use the '''BepiPred 2.0 server''', which was created here at DTU.
	<div style="background-color: lavender; border: solid thin grey;">		<div style="background-color: lavender; border: solid thin grey;">
	:'''Important Note:''' ~~Please run~~ the prediction ~~on the web server of the IEDB instead of~~ the ~~one at~~ DTU, ~~as our local servers had an update that~~ has ~~modified the results~~.		:'''Important Note:''' Before running the B-cell epitope prediction it will be needed to create a hotspot with your own MobilePhone as all the submissions from DTU will be runnning on a single queue, and not starting until the previous has finished.
	:~~Please select the method called "BepiPred 2.0"~~		:https://services.healthtech.dtu.dk/services/BepiPred-2.0/
	~~:http~~://~~tools~~.~~iedb~~.~~org~~/~~bcell~~/
	</div>		</div>

Carol: /* Epitope prediction */

2025-10-27T10:04:40Z

Epitope prediction

← Older revision		Revision as of 12:04, 27 October 2025
Line 167:		Line 167:
	# Go to the Structure section.		# Go to the Structure section.
	# Right-click the link labeled <u>RCSB-PDB</u> and open it in a new tab. This will take you to a PDB page.		# Right-click the link labeled <u>RCSB-PDB</u> and open it in a new tab. This will take you to a PDB page.
	# Here, you can find the sequence by clicking <u>Display Files</u> and choosing <u>FASTA Sequence</u>. You can ~~download~~ the sequence by ~~typing~~ on ~~the command line:~~		# Here, you can find the sequence by clicking <u>Display Files</u> and choosing <u>FASTA Sequence</u>. You can Download the sequence by Clicing on Download Files > FASTA Sequence.
	~~''save path-to-your-folder/my_sequence~~.~~fasta, format=fasta''~~

	<!--		<!--
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	-->		-->

	'''Question 4a''': What is the name of the PDB entry, and is it a crystal or NMR structure?		'''Question 4a''': What is the name of the PDB entry, and is it a crystal, EM or, NMR structure?

	'''Question 4b''': Report the FASTA sequence of the structure-determined Duffy binding domain in VAR2CSA.		'''Question 4b''': Report the FASTA sequence of the structure-determined Duffy binding domain in VAR2CSA.