Introduction

We provide a large number of tools for antibody informatics:

abYsis

Integrated database and analysis workbench

abYmod

Antibody modelling software

abYbank

Antibody sequence and structure data.
This includes:

• AbDb - pre-numbered structures from the PDB
• SACS - Summary of Antibody Crystal Structures
• EMBLIg - antibody sequences from EMBL-ENA
• Kabat - FASTA formatted sequences from Kabat (2000)
• AbPDBSeq - FASTA formatted antibody sequences from the PDB

Humanness (G)

Assess humanness against expressed sequences in Kabat divided into germline families

PAPS

Predict VH/VL packing angle

abYdraw

A downloadable software package for drawing antibody cartoons

The following are included within abYsis, but also available as standalone tools:

KabatMan

Query the Kabat sequence data

AbCheck

Test a sequence against the Kabat data for unusual residues

Chothia canonicals

Identify canonical classes for CDRs from your sequence

Human subgroups

Assign the human subgroup for your sequence

Humanness (H)

Assess humanness against expressed sequences in Kabat

Abnum

Apply standard numbering to sequences or structures

Information

Our pages of information on antibodies:

• The Kabat Numbering Scheme
• The Chothia Numbering Scheme
• The Martin (Enhanced Chothia) Numbering Scheme
• Table of CDR Definitions
• How to identify the CDRs by looking at a sequence
• Table of mean contact data
• Further information on numbering
• Antibody humanization patents

Information and links to accompany my book chapter Protein Sequence and Structure Analysis of Antibody Variable Domains. In: Antibody Engineering Lab Manual (Ed.: Duebel, S. and Kontermann, R., Springer-Verlag, Heidelberg). [Information] [Purchase]

The famous Kabat book is now available online as a scanned copy via Google Books: Elvin A. Kabat, Tai Te Wu, Carl Foeller, Harold M. Perry, Kay S. Gottesman (1991) Sequences of Proteins of Immunological Interest

abYsis

The abYsis database integrates sequence data from Kabat, IMGT and the wwPDB with structural data from the wwPDB and allows you to analyse your own sequences in the same manner.

abYmod

abYmod is a new antibody modelling program that makes extensive use of our extended definitions of canonical classes and combines this with prediction of VH/VL packing and an extended loop database for modelling CDR-H3.

abYbank

abYbank is a collection of sequence and structure data related to antibodies.

abYsis allows you to:

• Perform numbering and CDR definitions for your own sequences and analyse features relevant to humanization.
• Use data from the wwPDB to combine sequence searches with structural constraints. For example, one can ask for all the antibodies with a 10-residue Kabat CDR-L1 with a serine at H23 and an arginine within 10A of H36.

abYmod allows you to:

• Perform completely automated modelling.
• Intervene in the modelling process by correcting the numbering or selecting different templates.

abYbank provides:

• Sequences from EMBL-ENA
• Sequences from Kabat
• Sequences from PDB
• A summary of PDB structures
• Numbered structures and non-redundant sets

Access at www.abYsis.org

Commercial users wanting to use the system behind their firewall please refer to our collaborator web site: www.chemogenomix.com.

Access at abymod.abYsis.org

Commercial users wanting to use the system behind their firewall will soon be able to obtain a licence to the software via our collaborator web site: www.chemogenomix.com.

Access at www.abYbank.org