Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure
Open accessAbstract
Antibodies are capable of specifically recognizing and binding antigens. Identification of the antigen-binding site, commonly dubbed paratope, is of high importance both for medical and biological applications. To date, the identification of antigen-binding regions (ABRs) relies on tools for the identification of complementarity-determining regions (CDRs). However, we have shown that up to 22% of the residues that actually bind the antigen fall outside the traditionally defined CDRs. The Paratome web server predicts the ABRs of an antibody, given its amino acid sequence or 3D structure. It is based on a set of consensus regions derived from a structural alignment of a non-redundant set of all known antibody-antigen complexes. Given a query sequence or structure, the server identifies the regions in the query antibody that correspond to the consensus ABRs. An independent set of antibody-antigen complexes was used to test the server and it was shown to correctly identify at least 94% of the antigen-binding residues. The Paratome web server is freely available at http://www.ofranlab.org/paratome/.
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Tools such as Paratome can be used to identify positions in the framework region that might contribute to antigen recognition.
“Since not all paratope residues are constrained to the CDRs, tools such as Paratome [111, 159] can be used to identify positions in the framework region that might contribute to antigen recognition as well.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [111]
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- Authors
- Kunik, V., Ashkenazi, S., & Ofran, Y.
- Affiliations
- Bar-Ilan University (IL)
- Corresponding author
- Ofran, Yanay
- ORCID
- Ashkenazi, Shaul
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-06-06
- Volume
- 40
- Issue
- W1
- Pages
- W521-W524
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3394289
- OpenAlex
- W2150884352
- Cited by
- 132
- References
- 25
- Citations by year
- 2025: 7 · 2024: 8 · 2023: 9 · 2022: 17 · 2021: 23 · 2020: 15 · 2019: 11 · 2018: 14 · 2017: 6 · 2016: 8 · 2015: 4 · 2014: 5 · 2013: 5
- FWCI
- 3.38
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
- HighWire Press Open Archive (submittedVersion)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- antibody binding sites, antigen-binding region, immunoglobulins, hypervariable region, immune complexes, web server, structural alignment, consensus regions, epitope prediction
- MeSH terms
- Antigens, Binding Sites, Antibody, Protein Conformation, Software, Internet, Sequence Analysis, Protein, Complementarity Determining Regions
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