title: abYsis: Integrated Antibody Sequence and Structure-Management, Analysis, and Prediction.
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.
authors: Chemogenomix, 12 High Street, Easton on the Hill PE9 3LR, UK.
authors: Mark B
authors: MB
authors: Swindells
authors: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
authors: Craig T
authors: CT
authors: Porter
authors: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
authors: Matthew
authors: M
authors: Couch
authors: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
authors: Jacob
authors: J
authors: Hurst
authors: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
authors: K R
authors: KR
authors: Abhinandan
authors: Research Software Development Group, Research IT Services, University College London, Gower Street, London WC1E 6BT, UK.
authors: Jens H
authors: JH
authors: Nielsen
authors: Research Software Development Group, Research IT Services, University College London, Gower Street, London WC1E 6BT, UK.
authors: Gary
authors: G
authors: Macindoe
authors: Research Software Development Group, Research IT Services, University College London, Gower Street, London WC1E 6BT, UK.
authors: James
authors: J
authors: Hetherington
authors: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK. Electronic address: andrew@bioinf.org.uk.
authors: Andrew C R
authors: AC
authors: Martin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000906:Antibodies / Q000737:chemistry*; D022801:Complementarity Determining Regions; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D011499:Protein Processing, Post-Translational
chemical_list: D000906:Antibodies; D022801:Complementarity Determining Regions
keywords: antibodies; antibody humanization; bioinformatics and computational biology; databases; sequence analysis