ArticlePloS one2012
Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
32 citing papers in PubMed, 48 citations in OpenAlex.
- Prediction of Paratope-Epitope Pairs Using Convolutional Neural Networks.International journal of molecular sciences · 2024Article
- Mapping antibody footprints using binding profiles.Cell reports methods · 2023Article
- Unique Peptides of Cathelicidin-1 in the Early Detection of Mastitis-In Silico Analysis.International journal of molecular sciences · 2023Article
- Mechanism Exploration of Amyloid-β-42 Disaggregation by Single-Chain Variable Fragments of Alzheimer's Disease Therapeutic Antibodies.International journal of molecular sciences · 2023Article
- Computational Analysis of Antibody Paratopes for Antibody Sequences in Antibody Libraries.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Antibody CDR amino acids underlying the functionality of antibody repertoires in recognizing diverse protein antigens.Scientific reports · 2022Article
- Eradicating mesothelin-positive human gastric and pancreatic tumors in xenograft models with optimized anti-mesothelin antibody-drug conjugates from synthetic antibody libraries.Scientific reports · 2021Article
- Integrated in Silico and Experimental Approach towards the Design of a Novel Recombinant Protein Containing an Anti-HER2 scFv.International journal of molecular sciences · 2021Article
- Chemical Diversification of Simple Synthetic Antibodies.ACS chemical biology · 2021Article
- Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus.Nature communications · 2020Article
- Structural Analysis of Recent Allergen-Antibody Complexes and Future Directions.Current allergy and asthma reports · 2019Review
- Article
- Anti-ROR1 scFv-EndoG as a Novel Anti-Cancer Therapeutic DrugAsian Pacific journal of cancer prevention : APJCP · 2018Article
- Antibodyomics: bioinformatics technologies for understanding B-cell immunity to HIV-1.Immunological reviews · 2017Review
- High throughput cytotoxicity screening of anti-HER2 immunotoxins conjugated with antibody fragments from phage-displayed synthetic antibody libraries.Scientific reports · 2016Article
- Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms.PloS one · 2016Article
- Discovering neutralizing antibodies targeting the stem epitope of H1N1 influenza hemagglutinin with synthetic phage-displayed antibody libraries.Scientific reports · 2015Article
- Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Predominant structural configuration of natural antibody repertoires enables potent antibody responses against protein antigens.Scientific reports · 2015Article
- Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.PLoS computational biology · 2015Article
Corrections and comments
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Authors and funding
17 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor) interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antibody-antigen interfaces, for which the experimental validations are tractable with current high throughput synthetic antibody display technologies. Leave-one-out cross validation on the benchmark system yielded the accuracy, precision, recall (sensitivity) and specificity of the overall binary predictions to be 0.69, 0.45, 0.63, and 0.71 respectively, and the overall Matthews correlation coefficient of the 20 amino acid types in the 24 interface CDR positions was 0.312. The structure-based computational antibody design methodology was further tested with other antibodies binding to VEGF. The results indicate that the methodology could provide alternatives to the current antibody technologies based on animal immune systems in engineering therapeutic and diagnostic antibodies against predetermined antigen epitopes.
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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.