This page provides a set of links to tools described in my chapter entitled "Protein sequence and structure analysis of antibody variable domains" in the Springer Antibody Engineering Lab Manual.

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Introduction

Linking sequence and structure

• The Kabat numbering scheme
• The Chothia numbering scheme
• The Abhinandan (Updated Chothia) numbering scheme
• The IMGT numbering scheme
• The AHo numbering scheme

CDR definitions

• CDR definitions

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Procedures

Accessing Kabat sequence data

• Abysis
• The Kabat Database
• US Kabat download site
• UK Kabat download site
• KabatMan
• Subim download

Accessing IMGT sequence data

• Abysis
• The main IMGT server
• Nucleotide sequence analysis tools
• Protein sequence analysis tools

Accessing antibody structure data

• Abysis
• SACS
• AbDb
• The PDB

Assigning subgroups

• Subim human subgroup assignment

Identifying the CDRs

• CDR rules

Screening new antibody sequences

• SeqTest

Assigning canonicals

• Canonicals

Modelling antibodies

• abYmod
• WAM
• Rosetta Antibody
• MODELLER
• SwissModel