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SCALOP: sequence-based antibody canonical loop structure annotation

Wing Ki Wong, Guy Georges, Francesca Ros, Sebastian Kelm, Alan P Lewis, Bruck Taddese, Jinwoo Leem, Charlotte M Deane, Alfonso Valencia
2018 Bioinformatics  
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

Aleksandr Kovaltsuk, Matthew I. J. Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück, Charlotte M. Deane, Yanay Ofran
2020 PLoS Computational Biology  
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]

Aleksandr Kovaltsuk, Matthew I.J. Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück, Charlotte M Deane
2019 biorxiv/medrxiv   pre-print
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]

Marie Ghraichy, Jacob D Galson, Aleksandr Kovaltsuk, Valentin von Niederhaeusern, Jana Pachlopnik Schmid, Enkelejda Miho, Dominic F Kelly, Charlotte M Deane, Johannes Trueck
2019 bioRxiv   pre-print
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

Xiyao Long, Jeliazko R. Jeliazkov, Jeffrey J. Gray
2019 PeerJ  
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

Marie Ghraichy, Jacob D. Galson, Aleksandr Kovaltsuk, Valentin von Niederhäusern, Jana Pachlopnik Schmid, Mike Recher, Annaïse J. Jauch, Enkelejda Miho, Dominic F. Kelly, Charlotte M. Deane, Johannes Trück
2020 Frontiers in Immunology  
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