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Bioinformatics. 2019 May 15;35(10):1774-1776. doi: 10.1093/bioinformatics/bty877.

SCALOP: sequence-based antibody canonical loop structure annotation.

Author information

1
Department of Statistics, University of Oxford, Oxford, UK.
2
Roche Pharma Research and Early Development, Large Molecule Research Roche Innovation Center Munich, Penzberg, Germany.
3
UCB Pharma, Slough, UK.
4
Computational and Modelling Sciences, GlaxoSmithKline Research and Development, Stevenage, UK.
5
Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge, UK.

Abstract

MOTIVATION:

Canonical forms of the antibody complementarity-determining regions (CDRs) were first described in 1987 and have been redefined on multiple occasions since. The canonical forms are often used to approximate the antibody binding site shape as they can be predicted from sequence. A rapid predictor would facilitate the annotation of CDR structures in the large amounts of repertoire data now becoming available from next generation sequencing experiments.

RESULTS:

SCALOP annotates CDR canonical forms for antibody sequences, supported by an auto-updating database to capture the latest cluster information. Its accuracy is comparable to that of a standard structural predictor but it is 800 times faster. The auto-updating nature of SCALOP ensures that it always attains the best possible coverage.

AVAILABILITY AND IMPLEMENTATION:

SCALOP is available as a web application and for download under a GPLv3 license at opig.stats.ox.ac.uk/webapps/scalop.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

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