RosettaAntibody: antibody variable region homology modeling server
Open accessAbstract
The RosettaAntibody server (http://antibody.graylab.jhu.edu) predicts the structure of an antibody variable region given the amino-acid sequences of the respective light and heavy chains. In an initial stage, the server identifies and displays the most sequence homologous template structures for the light and heavy framework regions and each of the complementarity determining region (CDR) loops. Subsequently, the most homologous templates are assembled into a side-chain optimized crude model, and the server returns a picture and coordinate file. For users requesting a high-resolution model, the server executes the full RosettaAntibody protocol which additionally models the hyper-variable CDR H3 loop. The high-resolution protocol also relieves steric clashes by optimizing the CDR backbone torsion angles and by simultaneously perturbing the relative orientation of the light and heavy chains. RosettaAntibody generates 2000 independent structures, and the server returns pictures, coordinate files, and detailed scoring information for the 10 top-scoring models. The 10 models enable users to use rational judgment in choosing the best model or to use the set as an ensemble for further studies such as docking. The high-resolution models generated by RosettaAntibody have been used for the successful prediction of antibody-antigen complex structures.
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Antibody structures have conventionally been predicted using either physics-based modeling, such as MD simulations, or homology-based modeling, or a combined method, such as MODELLER.
“Antibody structures have conventionally been predicted using either physics-based modeling, such as MD simulations [38], or homologybased modeling [39], or a combined method, such as MODELLER [40].”
From Computational and artificial intelligence-based methods for antibody development (2023) · cites this paper as [39]
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- Authors
- Sircar, A., Kim, E. T., & Gray, J. J.
- Affiliations
- Johns Hopkins University (US)
- Corresponding author
- Gray, J. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-05-20
- Volume
- 37
- Issue
- Web Server
- Pages
- W474-W479
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC2703951
- OpenAlex
- W2045266215
- Cited by
- 161
- References
- 50
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 7 · 2023: 8 · 2022: 7 · 2021: 5 · 2020: 10 · 2019: 11 · 2018: 10 · 2017: 17 · 2016: 8 · 2015: 12 · 2014: 15 · 2013: 10 · 2012: 15
- FWCI
- 4.03
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Union Chimique Belge
- National Institutes of Health (GM-078221)
- National Institute of General Medical Sciences (R01GM073151, R01GM078221)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- immunoglobulin variable region, homology modeling, antibody structure prediction, hypervariable region, side-chain optimization, web server
- MeSH terms
- Algorithms, Immunoglobulin Variable Region, Immunoglobulin Heavy Chains, Immunoglobulin Light Chains, Models, Molecular, Software, User-Computer Interface, Sequence Homology, Amino Acid, Complementarity Determining Regions
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