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SCALOP: sequence-based antibody canonical loop structure annotation
2018
Bioinformatics
Preserved Fulltext
Results: SCALOP annotates CDR canonical forms for antibody sequences, supported by an autoupdating database to capture the latest cluster information. ...
The canonical forms are often used to approximate the antibody binding site shape as they can be predicted from sequence. ...
Since L2 loop structures are often invariant, we assign L2 loops of the dominant sequence length to a single canonical form; otherwise, it is not clustered. ...
doi:10.1093/bioinformatics/bty877
pmid:30321295
fatcat:3hyxkrwslfbdlck5svqdd6id2e
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice
2020
PLoS Computational Biology
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Most current analysis tools for antibody next-generation sequencing data work with primary sequence descriptors, leaving accompanying structural information unharnessed. ...
We show that B-cell types can be distinguished based solely on these structural properties. ...
SAAB+ uses SCALOP [21] to annotate non-CDR-H3 loop canonical classes. ...
doi:10.1371/journal.pcbi.1007636
pmid:32069281
pmcid:PMC7048297
fatcat:56gnyoti6rbfth4y3sld7yxq2e
Structural Diversity of B-Cell Receptor Repertoires along the B-cell Differentiation Axis in Humans and Mice
[article]
2019
biorxiv/medrxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Most current analysis tools for antibody next-generation sequencing data work with primary sequence descriptors, leaving accompanying structural information unharnessed. ...
We show that B-cell types can be distinguished based solely on these structural properties. ...
SAAB+ uses SCALOP [21] to annotate non-CDR-H3 loop canonical classes. ...
doi:10.1101/762880
fatcat:c2chl55cljcvtchu3e5gztmzt4
Maturation of naïve and antigen-experienced B-cell receptor repertoires with age
[article]
2019
bioRxiv
pre-print
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The file type is application/pdf.
Structural analysis revealed that the frequency of antibodies different from germline in shape increased with age. ...
B cells play a central role in adaptive immune processes, mainly through the production of antibodies. ...
canonical loop classes (CDR-H1 and CDR-H2) with SCALOP (20) and mapping the CDR-H3 loop sequences to known antibody structures using FREAD (21, 22) . ...
doi:10.1101/609651
fatcat:2cfiyfagjrbf7jh5zyyz7vyvei
Non-H3 CDR template selection in antibody modeling through machine learning
2019
PeerJ
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While RosettaAntibody and SAbPred do not explicitly assign query CDR sequences to clusters, two other approaches, PIGS and Kotai Antibody Builder, utilize sequence-based rules to assign CDR sequences to ...
While the manually curated sequence rules can identify better structural templates, because their curation requires extensive literature search and human effort, they lag behind the deposition of new antibody ...
is chosen as a template structure based on its sequence similarity to the query CDR loop. ...
doi:10.7717/peerj.6179
pmid:30648015
pmcid:PMC6330961
fatcat:s3tfhyujrfb4dj6axf4etbausm
Maturation of the Human Immunoglobulin Heavy Chain Repertoire With Age
2020
Frontiers in Immunology
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The most significant changes were observed in the first 10 years of life, and were characterized by altered immunoglobulin gene usage and an increased frequency of mutated antibodies structurally diverging ...
Older age was associated with an increased usage of downstream IgH constant region genes and fewer antibodies with self-reactive properties. ...
To annotate the numbered sequences with canonical loop class information, SAAB+ employs SCALOP (23) with the IMGT CDR definition (20) . ...
doi:10.3389/fimmu.2020.01734
pmid:32849618
pmcid:PMC7424015
fatcat:isfts3vis5hwvdgehs3tjtpcju