Characterize antibody chain variable domains by having Benchling detect and annotate antibody numbering schemes, CDR/FW regions, and potential sequence liability sites (PTMs).
If you’ve created or imported antibody protein sequences in Benchling, our Antibody Property Prediction visualizations can help annotate certain antibody-specific information. In addition to providing basic protein analysis capabilities, described here, Benchling can now automatically detect and annotate antibody chain variable domains with antibody numbering schemes, Complementarity Determining Regions (CDR) , framework (FW) regions, and potential sequence liability sites (PTMs).
To access these display features, open an amino acid sequence and click on the gear icon located in the upper right hand corner of the protein sequence map.
You can also access these display features on any protein alignment via a similar gear icon in the upper right hand corner of the protein alignment.
Viewing Antibody Numbering Schemes
Checking the display setting for Antibody Numbering will surface a blue annotation-like track denoting an alternative residue numbering index above your protein sequence.
Click the wrench icon to the right of the Antibody Numbering display setting to specify your desired antibody numbering scheme.
Benchling supports the following Antibody Numbering schemes:
Supported variable domain types:
Light chains (Kappa, Lambda)
T-Cell Receptors (Alpha, Beta, Delta, Gamma)TCRs can only be annotated for Human and MiceTCRs can only be annotated with the IMGT Numbering Scheme.
Human, Mouse, Rat, Rabbit, Rhesus, Pig, Alpaca
Benchling supports variable chain detection and annotation on sequences up to 2000 residues long.
[Please Note] - If the antibody numbering track isn’t showing the numbering index, zoom in on the sequence.
Viewing CDR and FW Regions
Checking the display setting for CDR Annotations will surface a blue and grey annotation-like track where blue regions denote CDRs and grey regions denote Framework Regions (FW).
Click the wrench icon to the right of the CDR Annotation display setting to specify which CDR definition set you would like Benchling to use when detecting CDR/FW regions.
Benchling supports the following Complementarity Determining Region (CDR) and Framework (FW) region definition sets:
Liability Sites (PTM Sites)
Checking the display setting for Liability Sites will surface a track of grey dots above the AA residues that mark certain AA patterns that may be prone to Post Translational Modifications (PTMs).
Hovering over a dot will both surface the PTM site that it denotes, as well as highlight all other PTM sites of the same type in your sequence.
Benchling detects and displays the following PTM sites and their AA patterns
N-linked Glycosylation: Arginine(N) followed by Serine(S) or Threonine(T), separated by a residue(X, where X is any AA except proline) (N-X-[S/T])
Asparagine Deamidation:Any Asparagine (N) in a CDR region (N in CDR)Any Asparagine(N) followed by Glycine(G), Serine(S), Threonine(T), or Asparagine(N) (NG|NS|NT|NN)
Aspartate Isomerization: Any Aspartic Acid(D) that is immediately followed by a Glycine(G), Serine(S), Threonine(T), Aspartic Acid (D) or Histidine(H) (DG|DS|DT|DD|DH)
Methionine Oxidation: Any Methionine (M)
Tryptophan OxidationAny Tryptophan (W)
[Please Note] We support two different patterns for Asparagine Deamidation. One will denote ANY Asparagine if it coincides with the CDR region (as defined by your current definition set). The other denotes any Asparagine if a G/S/T/D/H immediately follows it. Asparagines are more prone to deamidation if followed by one of these 5 AA’s, however within CDR regions, it has been shown that Asparagines not followed by G/S/T/D/H(non-canonical patterns) can also be deamidated.