Format

Send to

Choose Destination
Bioinformatics. 2018 Jun 15;34(12):2158-2160. doi: 10.1093/bioinformatics/bty055.

AbDesigner3D: a structure-guided tool for peptide-based antibody production.

Author information

1
Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
2
Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand.
3
Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, USA.

Abstract

Summary:

We present AbDesigner3D, a new tool for identification of optimal immunizing peptides for antibody production using a peptide-based strategy. AbDesigner3D integrates 3D structural data from the Protein Data Bank (PDB) with UniProt data, which includes basic sequence data, post-translational modification sites, SNP occurrences and more. Other features, such as uniqueness and conservation scores, are calculated based on sequences from UniProt. The 3D visualization capabilities allow an intuitive interface, while an abundance of quantitative output simplifies the process of comparing immunogen peptides. Important quantitative features added in this tool include calculation and display of accessible surface area (ASA) and protein-protein interacting residues (PPIR). The specialized data visualization features of AbDesigner3D will greatly assist users to optimize their choice of immunizing peptides.

Availability and implementation:

AbDesigner3D is freely available at http://sysbio.chula.ac.th/AbDesigner3D or https://hpcwebapps.cit.nih.gov/AbDesigner3D/.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
29408997
PMCID:
PMC6248693
DOI:
10.1093/bioinformatics/bty055
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center