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abYsis: Integrated Antibody Sequence and Structure-Management, Analysis, and Prediction

Swindells, MB; Porter, CT; Couch, M; Hurst, J; Abhinandan, KR; Nielsen, JH; Macindoe, G; ... Martin, AC; + view all (2017) abYsis: Integrated Antibody Sequence and Structure-Management, Analysis, and Prediction. Journal of Molecular Biology , 429 (3) pp. 356-364. 10.1016/j.jmb.2016.08.019. Green open access

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Abstract

abYsis is a web-based antibody research system that includes an integrated database of antibody sequence and structure data. The system can be interrogated in numerous ways-from simple text and sequence searches to sophisticated queries that apply 3D structural constraints. The publicly available version includes pre-analyzed sequence data from the European Molecular Biology Laboratory European Nucleotide Archive (EMBL-ENA) and Kabat as well as structure data from the Protein Data Bank. A researcher's own sequences can also be analyzed through the web interface. A defining characteristic of abYsis is that the sequences are automatically numbered with a series of popular schemes such as Kabat and Chothia and then annotated with key information such as complementarity-determining regions and potential post-translational modifications. A unique aspect of abYsis is a set of residue frequency tables for each position in an antibody, allowing "unusual residues" (those rarely seen at a particular position) to be highlighted and decisions to be made on which mutations may be acceptable. This is especially useful when comparing antibodies from different species. abYsis is useful for any researcher specializing in antibody engineering, especially those developing antibodies as drugs. abYsis is available at www.abysis.org.

Type: Article
Title: abYsis: Integrated Antibody Sequence and Structure-Management, Analysis, and Prediction
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.jmb.2016.08.019
Publisher version: http://dx.doi.org/10.1016/j.jmb.2016.08.019
Language: English
Additional information: © 2016 Published by Elsevier Ltd. This manuscript version is published under a Creative Commons Attribution Non-commercial Non-derivative 4.0 International licence (CC BY-NC-ND 4.0). This licence allows you to share, copy, distribute and transmit the work for personal and non-commercial use providing author and publisher attribution is clearly stated. Further details about CC BY licences are available at http://creativecommons.org/licenses/by/4.0. Access may be initially restricted by the publisher.
Keywords: Antibodies, antibody humanization, bioinformatics and computational biology, databases, sequence analysis
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: https://discovery.ucl.ac.uk/id/eprint/1508393
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