Exercise:AntibodyStructurePrediction - Revision history

Carol: /* Identifying mutations in the antibody sequence */

2026-10-21T03:17:08Z

Identifying mutations in the antibody sequence

← Older revision		Revision as of 04:17, 21 October 2026
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	Unfortunately today the server has a planning update so the output of the tool are provided below		Unfortunately today the server has a planning update so the output of the tool are provided below

	[[image:Imgt_GapAlign_results_VH.png\|~~500px~~\|center]]		[[image:Imgt_GapAlign_results_VH.png\|1000px\|center]]

	[[image:Imgt_GapAlign_results_VL.png\|~~500px~~\|center]]		[[image:Imgt_GapAlign_results_VL.png\|1000px\|center]]

	'''Q8: Which Mutations are located inside/near the CDRs? Which are the ones that are most likely to have an impact on the binding of the antibody?''' ''A qualitative answer is sufficient''		'''Q8: Which Mutations are located inside/near the CDRs? Which are the ones that are most likely to have an impact on the binding of the antibody?''' ''A qualitative answer is sufficient''

Carol: /* Identifying mutations in the antibody sequence */

2026-10-21T03:16:53Z

Identifying mutations in the antibody sequence

← Older revision		Revision as of 04:16, 21 October 2026
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	Use the [http://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.cgi Domain Gap Align tool] identify the somatic mutations in the V and J regions. You need to use the amino acid sequence and select human as the source organism. In PyMol, show the mutations as sticks (main chain and side chain) and color them green.		Use the [http://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.cgi Domain Gap Align tool] identify the somatic mutations in the V and J regions. You need to use the amino acid sequence and select human as the source organism. In PyMol, show the mutations as sticks (main chain and side chain) and color them green.

			Unfortunately today the server has a planning update so the output of the tool are provided below

			[[image:Imgt_GapAlign_results_VH.png\|500px\|center]]

			[[image:Imgt_GapAlign_results_VL.png\|500px\|center]]

	'''Q8: Which Mutations are located inside/near the CDRs? Which are the ones that are most likely to have an impact on the binding of the antibody?''' ''A qualitative answer is sufficient''		'''Q8: Which Mutations are located inside/near the CDRs? Which are the ones that are most likely to have an impact on the binding of the antibody?''' ''A qualitative answer is sufficient''


	== Part 4 — Electrostatic properties of the antigen-binding site ==		== Part 4 — Electrostatic properties of the antigen-binding site ==

Carol: /* Visualizing the antigen-binding site */

2026-10-21T02:25:34Z

Visualizing the antigen-binding site

← Older revision		Revision as of 03:25, 21 October 2026
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	== Part 2 — Exploring the antibody structure in PyMOL ==		== Part 2 — Exploring the antibody structure in PyMOL ==

	=== Visualizing the antigen-binding site ===		=== Visualizing the antigen-binding site (ABS) ===

	Download the pdb file and open it with pymol. There is a small "S" bottom right, it shows/hides the sequence. Show the whole protein as cartoon and color by chain. Select and color in red all the CDRs. (the selected residues appear as the "sele" item in the menu). The CDR definition can be seen in the alignment generated by Lyra.		Download the pdb file and open it with pymol. There is a small "S" bottom right, it shows/hides the sequence. Show the whole protein as cartoon and color by chain. Select and color in red all the CDRs. (the selected residues appear as the "sele" item in the menu). The CDR definition can be seen in the alignment generated by Lyra.

Carol: /* Part 1 — Identify the antibody regions */

2026-10-21T02:24:12Z

Part 1 — Identify the antibody regions

← Older revision		Revision as of 03:24, 21 October 2026
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	'''Q4: Do the loops/CDR have the same length in target and template? What does it mean, in terms of expected accuracy?'''		'''Q4: Do the loops/CDR have the same length in target and template? What does it mean, in terms of expected accuracy?'''

			=== Selection of structural templates ===

	Now, look at the templates automatically selected by Lyra to build the final model.		Now, look at the templates automatically selected by Lyra to build the final model.

	'''Q5: How many templates were used? Which is the region for which the template is more dissimilar to the target sequence?'''		'''Q5: How many templates were used? Which is the region for which the template is more dissimilar to the target sequence?'''


			== Part 2 — Exploring the antibody structure in PyMOL ==

			=== Visualizing the antigen-binding site ===

	Download the pdb file and open it with pymol. There is a small "S" bottom right, it shows/hides the sequence. Show the whole protein as cartoon and color by chain. Select and color in red all the CDRs. (the selected residues appear as the "sele" item in the menu). The CDR definition can be seen in the alignment generated by Lyra.		Download the pdb file and open it with pymol. There is a small "S" bottom right, it shows/hides the sequence. Show the whole protein as cartoon and color by chain. Select and color in red all the CDRs. (the selected residues appear as the "sele" item in the menu). The CDR definition can be seen in the alignment generated by Lyra.

	'''Q6: What is the general shape of the ABS: flat, a pocket, a mountain or a groove?''' ''It can help to show the antibody as surface''		'''Q6: What is the general shape of the ABS: flat, a pocket, a mountain or a groove?''' ''It can help to show the antibody as surface''

			=== CDR loop structure ===

	'''Q7: Which loop is the longest and protruding the most? Is this the most common case?'''		'''Q7: Which loop is the longest and protruding the most? Is this the most common case?'''


			== Part 3 — Somatic mutations ==

			=== Identifying mutations in the antibody sequence ===

	Use the [http://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.cgi Domain Gap Align tool] identify the somatic mutations in the V and J regions. You need to use the amino acid sequence and select human as the source organism. In PyMol, show the mutations as sticks (main chain and side chain) and color them green.		Use the [http://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.cgi Domain Gap Align tool] identify the somatic mutations in the V and J regions. You need to use the amino acid sequence and select human as the source organism. In PyMol, show the mutations as sticks (main chain and side chain) and color them green.

	'''Q8: Which Mutations are located inside/near the CDRs? Which are the ones that are most likely to have an impact on the binding of the antibody?''' ''A qualitative answer is sufficient''		'''Q8: Which Mutations are located inside/near the CDRs? Which are the ones that are most likely to have an impact on the binding of the antibody?''' ''A qualitative answer is sufficient''


			== Part 4 — Electrostatic properties of the antigen-binding site ==

			=== Visualizing the electrostatic potential ===

	Generate the electrostatic potentials of the Ig ('''A'''ction -> generate -> vacuum electrostatic -> protein contact potentials).		Generate the electrostatic potentials of the Ig ('''A'''ction -> generate -> vacuum electrostatic -> protein contact potentials).
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	''highlight them in the sequence and look for charged residues such as K, R, D, E''		''highlight them in the sequence and look for charged residues such as K, R, D, E''

			=== Modifying the electrostatic properties (optional) ===

	'''Q10: (optional) Mutate some residues in order to have a positive charge in the middle of the antigen binding site, then recalculate the electrostatic potentials. Can you see the changes?'''		'''Q10: (optional) Mutate some residues in order to have a positive charge in the middle of the antigen binding site, then recalculate the electrostatic potentials. Can you see the changes?'''


			== Part 5 — Comparing antibody modelling approaches ==

			=== LYRA versus ABodyBuilder2 ===

	'''Q11: Go to the AbodyBuilder 2 site and make a new structure prediction. Download the PDB file and compare with the model generated by LYRA. Can you see some differences?'''		'''Q11: Go to the AbodyBuilder 2 site and make a new structure prediction. Download the PDB file and compare with the model generated by LYRA. Can you see some differences?'''

Carol: /* Part 1 — Identify the antibody regions */

2026-10-21T02:14:42Z

Part 1 — Identify the antibody regions

← Older revision		Revision as of 03:14, 21 October 2026
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	\| ...		\| ...
	\|}		\|}


	Note that after the Regions there is an extra template used for packing the whole structure.		Note that after the Regions there is an extra template used for packing the whole structure.

Carol at 02:14, 21 October 2026

2026-10-21T02:14:20Z

← Older revision		Revision as of 03:14, 21 October 2026
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	'''Q2: What is the light chain type? Is it the most common in humans?'''		'''Q2: What is the light chain type? Is it the most common in humans?'''

			=== Sequence alignment and CDR modelling ===

	Focus on the sequence alignment used to generate the model. You can find it in one of the tabs in Lyra website, as well as in the PDB file itself.		Focus on the sequence alignment used to generate the model. You can find it in one of the tabs in Lyra website, as well as in the PDB file itself.

Carol: /* Part 1 — Identify the antibody regions */

2026-10-21T02:08:44Z

Part 1 — Identify the antibody regions

← Older revision		Revision as of 03:08, 21 October 2026
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	Now answer the following questions:		Now answer the following questions:

	'''Q1:~~'''~~ what is the sequence similarity of the best H and L templates for the framework (FW)?		'''Q1: what is the sequence similarity of the best H and L templates for the framework (FW)?'''

	'''Q2: What is the light chain type? Is it the most common in humans?'''		'''Q2: What is the light chain type? Is it the most common in humans?'''

Carol: /* Part 1 — Identify the antibody regions */

2026-10-21T02:08:19Z

Part 1 — Identify the antibody regions

← Older revision		Revision as of 03:08, 21 October 2026
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	~~'''~~Note~~'''~~ that after the Regions there is an extra template used for packing the whole structure.		Note that after the Regions there is an extra template used for packing the whole structure.

			Explore the output page and the different tabs - check the PDB file, Log, and manual selection ones to find this info.


	Now answer the following questions:		Now answer the following questions:

	'''Q1: what is the sequence similarity of the best H and L templates for the framework (FW)?~~'''~~		'''Q1:''' what is the sequence similarity of the best H and L templates for the framework (FW)?

	~~''hint: In the output page you have a few tabs - check the PDB file, Log, and manual selection ones to find this info.''~~

	'''Q2: What is the light chain type? Is it the most common in humans?'''		'''Q2: What is the light chain type? Is it the most common in humans?'''

Carol: /* Part 1 — Identify the antibody regions */

2026-10-21T02:06:14Z

Part 1 — Identify the antibody regions

← Older revision		Revision as of 03:06, 21 October 2026
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	\| ...		\| ...
	\|}		\|}


			'''Note''' that after the Regions there is an extra template used for packing the whole structure.

			Now answer the following questions:

	'''Q1: what is the sequence similarity of the best H and L templates for the framework (FW)?'''		'''Q1: what is the sequence similarity of the best H and L templates for the framework (FW)?'''

Carol: /* Part 1 — Identify the antibody regions */

2026-10-21T02:03:51Z

Part 1 — Identify the antibody regions

← Older revision		Revision as of 03:03, 21 October 2026
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	Insert the light and heavy chains in the proper text area and submit. After a few seconds you will arrive to the output page, where the alignment and all the templates are displayed.		Insert the light and heavy chains in the proper text area and submit. After a few seconds you will arrive to the output page, where the alignment and all the templates are displayed.

			Note that for each Region of each chain of the antibody a Template has been found.

			{\| class="wikitable"
			! Region
			! Templates
			\|-
			\| Framework
			\| ...
			\|-
			\| Loop 1 (CDR1)
			\| ...
			\|-
			\| Loop 2 (CDR2)
			\| ...
			\|-
			\| Loop 3 (CDR3)
			\| ...
			\|}

	'''Q1: what is the sequence similarity of the best H and L templates for the framework (FW)?'''		'''Q1: what is the sequence similarity of the best H and L templates for the framework (FW)?'''