AbDesigner

Select Input Type question_blue

Gene Symbol	(e.g. AQP2)
Swiss-Prot Accession Number	(e.g. P41181)
Swiss-Prot Entry Name	(e.g. AQP2_HUMAN)
FASTA Amino Acid Sequence

To specify a protein for analysis, the program accepts the following types of input:

Official Gene Symbol
Swiss-Prot Accession Number
Swiss-Prot Entry Name

from any of the following seven species:

Homo sapiens
Rattus norvegicus
Mus musculus
Drosophila melanogaster
Caenorhabditis elegans
Saccharomyces cerevisiae
Arabidopsis thaliana

Proteins from other species can be analyzed by entering the sequence of that protein FASTA format (This should be avoided when analyzing proteins from the above seven species because of the limitations associated with submitting a FASTA amino acid sequence as described in the Frequently Asked Questions).

Enter Input question_blue

Autocomplete widget provides suggestions while you type into the field. (Does not work with FASTA input)
The suggestions are displayed when at least two characters are entered into the field.

Peptide Length question_blue

(5-50 amino acids)

A user-defined sequence length for production of synthetic peptides for immunization can be set from 5 to 50 amino acids.
A peptide of 10-25 amino acids is typically used.
A longer sequence can provide a greater likelihood of producing a potent antibody by virtue of the fact that it contains more potential epitopes, but by the same token there is a greater chance that it will produce IgG clones with lower specificity.
Furthermore, the cost of peptide synthesis often increases substantially with larger peptides.

Epitope Length question_blue

(≤ Peptide Length, minimum 5 amino acids)

A user-defined linear 'Epitope Length' can be set from 5 amino acids to the full length of the peptide.
Only the 5-10 amino acids in each hypervariable region form the antigen-binding site of an antibody molecule. As a result, the size of the antigenic determinant (epitope) that an antibody recognizes is generally comparably small.
The 'Epitope Length' is used for determination of uniqueness and conservation of a peptide as described in the Frequently Asked Questions.

AbDesigner is a tool for analyzing the amino acid sequence of a given protein to identify optimal immunizing peptides for production of antibodies.

AbDesigner displays the information needed for choice of immunizing peptides, allowing the user to recognize trade-offs between immunogenicity, specificity, animal species targets, and post-translational modifications.

Disclaimer: Recommended peptides are not guaranteed to successfully produce antibodies. Users should consider all factors when planning an antibody production project including the conjugation method, immunization protocol, and antibody purification procedure.

Accessibility: Because of the complex intersections and simultaneous display protein sequences, using the AbDesigner requires the use of a mouse, and therefore presents known accessibility issues. The NHLBI is committed to providing this information for people who cannot use the tool as designed. For more information or assistance please contact Dr. Trairak Pisitkun at 301-496-8319, pisitkut@nhlbi.nih.gov or Dr. Mark Knepper at 301-496-3064, knepperm@nhlbi.nih.gov.