ArticleProteins2017
High-accuracy modeling of antibody structures by a search for minimum-energy recombination of backbone fragments.
Article in Proteins, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 24 citations in OpenAlex.
- Computational optimization of antibody humanness and stability by systematic energy-based ranking.Nature biomedical engineering · 2024Article
- Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens.Journal of chemical theory and computation · 2023Review
- VInternational journal of molecular sciences · 2022Review
- Article
- The neutralization potency of anti-SARS-CoV-2 therapeutic human monoclonal antibodies is retained against viral variants.Cell reports · 2021Article
- Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.Biochemistry · 2021Review
- Toward Biotherapeutics Formulation Composition Engineering using Site-Identification by Ligand Competitive Saturation (SILCS).Journal of pharmaceutical sciences · 2021Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV.Nature medicine · 2019Article
- Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces.PLoS computational biology · 2019Article
- AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains.Bioinformatics (Oxford, England) · 2019Article
- Understanding and overcoming trade-offs between antibody affinity, specificity, stability and solubility.Biochemical engineering journal · 2018Article
- A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen.Scientific reports · 2018Article
- Principles for computational design of binding antibodies.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Current methods for antibody structure prediction rely on sequence homology to known structures. Although this strategy often yields accurate predictions, models can be stereo-chemically strained. Here, we present a fully automated algorithm, called AbPredict, that disregards sequence homology, and instead uses a Monte Carlo search for low-energy conformations built from backbone segments and rigid-body orientations that appear in antibody molecular structures. We find cases where AbPredict selects accurate loop templates with sequence identity as low as 10%, whereas the template of highest sequence identity diverges substantially from the query's conformation. Accordingly, in several cases reported in the recent Antibody Modeling Assessment benchmark, AbPredict models were more accurate than those from any participant, and the models' stereo-chemical quality was consistently high. Furthermore, in two blind cases provided to us by crystallographers prior to structure determination, the method achieved <1.5 Ångstrom overall backbone accuracy. Accurate modeling of unstrained antibody structures will enable design and engineering of improved binders for biomedical research directly from sequence. Proteins 2016; 85:30-38. © 2016 Wiley Periodicals, Inc.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.