Antibody Studio: Numbering, Liabilities, Humanization and CDR Redesign to a Cloning-Ready Construct
Video · 2:34 · Published November 3, 2026 · Talindrew team
About this video
Antibody tools stop at annotation; this one ends at a DNA sequence you can put in cells. One antibody, the two variable domains of trastuzumab, goes the whole way in two and a half minutes. Numbering finds both domains and marks the six CDRs, calling the closest human germline as IGHV3-66. Switching IMGT for Kabat moves the boundaries on the same residues, because a CDR is a property of the scheme. The liability scan finds 14 possible sites, 7 of them in a CDR and 5 already carried by the germline. Humanness scores every position with Sapiens. Humanization grafts the loops onto the closest human framework in 8 substitutions and says plainly that the graft created one new liability. ABodyBuilder2 folds the Fv on real compute and pins every liability onto the 3D model, AntiFold samples 11 CDR variants against that backbone, and the expression construct back-translates to 420 bp of DNA for CHO with a human Ig leader, designed around 13 restriction sites, then opens in the sequence editor with the leader and all three loops annotated, ready to clone.
What you will learn
- Number antibody variable domains and annotate the six CDRs, in IMGT, Kabat, Chothia, Martin, Aho or Wolfguy
- Find sequence liabilities: deamidation, isomerisation, oxidation, glycosylation sequons and unpaired cysteines, and see which the germline already carried
- Score humanness per position and graft the CDRs onto the closest human framework
- Fold the Fv with ABodyBuilder2 and see which liabilities are actually on the surface
- Redesign a CDR with AntiFold against that backbone
- Back-translate to an expression construct for CHO, HEK293, E. coli or yeast and open it in the cloning suite
Transcript
- 0:00
Antibody Studio · paste an Fv
An antibody is easy to draw and hard to make. Talindrew takes one from a sequence to a construct you can put in cells. This is Antibody Studio. Start from a real antibody: the two variable domains of trastuzumab.
- 0:23
Numbering, CDRs and the germline call
Numbering finds both domains and marks the six loops that do the binding. The closest human germline is IGHV3-66, which is where trastuzumab really came from.
- 0:38
Scheme is not CDR definition
And a CDR is a property of the scheme, not of the molecule. Switch IMGT for Kabat and the same residues get different boundaries.
- 0:49
Sequence liabilities
Liabilities reads the sequence for the chemistry that goes wrong in manufacturing. Fourteen possible sites here: seven of them in a CDR, five of them already carried by the germline.
- 1:04
Humanness
Humanness asks a different question: how like a human antibody does every position look? That is a model's opinion, so it is never drawn in the alarm colour a liability gets.
- 1:17
Humanization
Humanize grafts those loops onto the closest human framework. Eight substitutions, humanness up three points, and it says plainly that the graft created one new liability.
- 1:31
Fv structure with ABodyBuilder2
Structure folds the variable domains with ABodyBuilder2, on real compute, in well under a minute, and pins every liability onto the model, so you can see which ones are actually on the surface.
- 1:47
CDR redesign with AntiFold
And on that backbone, AntiFold redesigns a loop: eleven variants, each scored for how well it fits the structure it was given, which is not a promise that binding survives, and the panel says so.
- 2:02
The expression construct
Then the part the annotation tools stop short of: the construct. Pick the host and the leader, and it back-translates into DNA, designed around thirteen restriction sites.
- 2:16
Straight into cloning
And it goes straight to the bench side of the app: a real sequence, with the leader and all three loops annotated on it, ready to clone. Talindrew. From a sequence to something you can clone.
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