Exercise:AntibodyStructurePrediction ans - Revision history

Carol at 03:00, 21 October 2026

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	These answers refer to the SI135 antibody and the LYRA model generated from its heavy- and light-chain variable-region sequences. Residue numbering is identified as IMGT or PDB numbering where relevant.		These answers refer to the SI135 antibody and the LYRA model generated from its heavy- and light-chain variable-region sequences. Residue numbering is identified as IMGT or PDB numbering where relevant.

			https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AD8166000282F67166ED625&wait=20

	== Part 1 — Antibody modelling with LYRA ==		== Part 1 — Antibody modelling with LYRA ==

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Q6. Shape of the antigen-binding site

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	=== Q6. Shape of the antigen-binding site ===		=== Q6. Shape of the antigen-binding site ===

	'''~~Expected answer~~:'''		'''Answer:'''

	The antigen-binding site is formed by the six CDR loops.		The antigen-binding site is formed by the six CDR loops.

	Its overall shape ~~should~~ be classified by displaying the predicted antibody as a molecular surface and examining the arrangement of these loops.		Its overall shape can be classified by displaying the predicted antibody as a molecular surface and examining the arrangement of these loops.

	'''SI135 classification:''' Pocket-like		'''SI135 classification:''' Pocket-like

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Q6. Shape of the antigen-binding site

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	Its overall shape should be classified by displaying the predicted antibody as a molecular surface and examining the arrangement of these loops.		Its overall shape should be classified by displaying the predicted antibody as a molecular surface and examining the arrangement of these loops.

	'''SI135 classification:''' ~~To be confirmed from the PyMOL surface representation.~~		'''SI135 classification:''' Pocket-like

	~~The LYRA sequence alignments do not establish whether the binding site is flat, pocket-like, groove-like or mountain-like.~~		Note that this classification is qualitative.

	~~The~~ classification is qualitative~~, and students should justify their answer based on the model~~.

	=== Q7. Longest and most protruding CDR ===		=== Q7. Longest and most protruding CDR ===

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Q9. Charged CDR residues

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	\|}		\|}

	~~Students~~ can highlight the main charged CDR residues using the following PyMOL commands:		You can highlight the main charged CDR residues using the following PyMOL commands:

	<pre>		<pre>

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Q3. Sequence differences between target and templates

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	In the light-chain framework alignment, a D → K substitution near the C-terminus also reverses the side-chain charge.		In the light-chain framework alignment, a D → K substitution near the C-terminus also reverses the side-chain charge.

	'''~~Observation~~:''' The impact of a substitution depends not only on its BLOSUM score but also on its structural location and whether the residue is buried or exposed.		'''Note:''' The impact of a substitution depends not only on its BLOSUM score but also on its structural location and whether the residue is buried or exposed.

	=== Q4. CDR loop lengths and expected accuracy ===		=== Q4. CDR loop lengths and expected accuracy ===

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Q4. CDR loop lengths and expected accuracy

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	This introduces additional uncertainty in the loop conformation.		This introduces additional uncertainty in the loop conformation.

	'''~~Teaching point~~:''' Matching loop length does not guarantee that the target and template have the same three-dimensional conformation.		'''Note:''' Matching loop length does not guarantee that the target and template have the same three-dimensional conformation.

	=== Q5. Number of templates and most dissimilar region ===		=== Q5. Number of templates and most dissimilar region ===

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Q3. Sequence differences between target and templates

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	In the light-chain framework alignment, a D → K substitution near the C-terminus also reverses the side-chain charge.		In the light-chain framework alignment, a D → K substitution near the C-terminus also reverses the side-chain charge.

	'''~~Teaching point~~:''' The impact of a substitution depends not only on its BLOSUM score but also on its structural location and whether the residue is buried or exposed.		'''Observation:''' The impact of a substitution depends not only on its BLOSUM score but also on its structural location and whether the residue is buried or exposed.

	=== Q4. CDR loop lengths and expected accuracy ===		=== Q4. CDR loop lengths and expected accuracy ===

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	__TOC__		__TOC__

	= Antibody Structure Modelling ~~— Teacher's~~ Answers =		= Antibody Structure Modelling Answers =

	'''Case study:''' SI135 antibody from chronic lymphocytic leukemia (CLL)		'''Case study:''' SI135 antibody from chronic lymphocytic leukemia (CLL)
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	'''LYRA prediction:''' [https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AD8166000282F67166ED625&wait=20 View the original modelling job]		'''LYRA prediction:''' [https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AD8166000282F67166ED625&wait=20 View the original modelling job]

	~~''This page provides expected answers to Q1–Q11. Values marked [TO VERIFY] require inspection of the LYRA model, sequence alignment, or additional analyses.''~~

	== Part 1 — Antibody modelling with LYRA ==		== Part 1 — Antibody modelling with LYRA ==