ArticleBioinformatics (Oxford, England)2019
SCALOP: sequence-based antibody canonical loop structure annotation.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 38 citations in OpenAlex.
- Tokenizing loops of antibodies.mAbs · 2026Article
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- LICHEN enables light-chain immunoglobulin sequence generation conditioned on the heavy chain and experimental needs.Communications biology · 2026Article
- Artificial intelligence advancements in monoclonal antibody development technology.Frontiers in immunology · 2026Review
- Revolutionizing oncology: the role of Artificial Intelligence (AI) as an antibody design, and optimization tools.Biomarker research · 2025Review
- T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity.Communications biology · 2025Article
- Antibody numbering schemes: advances, comparisons and tools for antibody engineering.Protein engineering, design & selection : PEDS · 2025Review
- Identification of Conserved Linear Epitopes on Viral Protein 2 of Foot-and-Mouth Disease Virus Serotype O by Monoclonal Antibodies 6F4.D11.B6 and 8D6.B9.C3.Antibodies (Basel, Switzerland) · 2024Article
- Building Representation Learning Models for Antibody Comprehension.Cold Spring Harbor perspectives in biology · 2024Review
- Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms.Frontiers in immunology · 2024Article
- Article
- Learned features of antibody-antigen binding affinity.Frontiers in molecular biosciences · 2023Article
- Specific attributes of the VFrontiers in immunology · 2023Article
- Article
- Deciphering the language of antibodies using self-supervised learning.Patterns (New York, N.Y.) · 2022Article
- Robustification of RosettaAntibody and Rosetta SnugDock.PloS one · 2021Article
- Computational approaches to therapeutic antibody design: established methods and emerging trends.Briefings in bioinformatics · 2020Review
- Article
- A Review of Deep Learning Methods for Antibodies.Antibodies (Basel, Switzerland) · 2020Review
- Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice.PLoS computational biology · 2020Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
motivationCanonical 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.
resultsSCALOP 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.