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J Mol Biol. 2017 Feb 3;429(3):356-364. doi: 10.1016/j.jmb.2016.08.019. Epub 2016 Aug 22.

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

Author information

1
Chemogenomix, 12 High Street, Easton on the Hill PE9 3LR, UK.
2
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
3
Research Software Development Group, Research IT Services, University College London, Gower Street, London WC1E 6BT, UK.
4
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK. Electronic address: andrew@bioinf.org.uk.

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.

KEYWORDS:

antibodies; antibody humanization; bioinformatics and computational biology; databases; sequence analysis

PMID:
27561707
DOI:
10.1016/j.jmb.2016.08.019
[Indexed for MEDLINE]

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