ReviewNature protocols2023
The ClusPro AbEMap web server for the prediction of antibody epitopes.
Review in Nature protocols, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 38 citations in OpenAlex.
- Article
- Combining AI Structure Prediction and Integrative Modeling for Nanobody-Antigen Complexes.Journal of chemical information and modeling · 2026Article
- Host immune network-guided reverse vaccinology approach for prioritizing candidate antigens in Schistosoma japonicum-associated liver fibrosis.PLoS neglected tropical diseases · 2026Article
- Immunoinformatics Design of a Broad-Spectrum Multi-Epitope Vaccine Targeting HA2 and M1 of H9N2 AIV.Microorganisms · 2026Article
- Targeting PD-1Science advances · 2026Article
- Exploring Trop-2-Nanobody PPI Interactions through Molecular Dynamics Simulations and Biovalidations.ACS omega · 2026Article
- Rab14 restricts pathogens by promoting V-ATPase lysosomal delivery to drive lysosomal acidification.Nature communications · 2026Article
- Immunoinformatics and molecular modeling approaches to design a multi-epitope vaccine against Tibrovirus Congo.Open medicine (Warsaw, Poland) · 2026Article
- Improving B-cell epitope prediction.Drug discovery today · 2025Review
- Insights Into Kaposi Sarcoma-Associated Herpesvirus-Specific Humoral Responses.Journal of medical virology · 2025Review
- Computational and experimental discovery of peptide inhibitors targeting survivin for therapeutic potential in cancer.Scientific reports · 2025Article
- Dockground: The Resource Expands to Protein-RNA Interactome.Journal of molecular biology · 2025Article
- Article
- Interaction between bacterial phytochromes Agp1 and Agp2 of Agrobacterium fabrum by fluorescence resonance energy transfer and docking studies.FEBS letters · 2025Article
- Clinicopathological andCurrent medicinal chemistry · 2025Article
- Applying computational protein design to therapeutic antibody discovery - current state and perspectives.Frontiers in immunology · 2025Review
- The evolutionary features and roles of single nucleotide variants and charged amino acid mutations in influenza outbreaks during NPI period.Scientific reports · 2024Article
- Peptide Antibodies: Current Status.Methods in molecular biology (Clifton, N.J.) · 2024Article
- AlphaFold2 in biomedical research: facilitating the development of diagnostic strategies for disease.Frontiers in molecular biosciences · 2024Review
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
Abstract
Antibodies play an important role in the immune system by binding to molecules called antigens at their respective epitopes. These interfaces or epitopes are structural entities determined by the interactions between an antibody and an antigen, making them ideal systems to analyze by using docking programs. Since the advent of high-throughput antibody sequencing, the ability to perform epitope mapping using only the sequence of the antibody has become a high priority. ClusPro, a leading protein-protein docking server, together with its template-based modeling version, ClusPro-TBM, have been re-purposed to map epitopes for specific antibody-antigen interactions by using the Antibody Epitope Mapping server (AbEMap). ClusPro-AbEMap offers three different modes for users depending on the information available on the antibody as follows: (i) X-ray structure, (ii) computational/predicted model of the structure or (iii) only the amino acid sequence. The AbEMap server presents a likelihood score for each antigen residue of being part of the epitope. We provide detailed information on the server's capabilities for the three options and discuss how to obtain the best results. In light of the recent introduction of AlphaFold2 (AF2), we also show how one of the modes allows users to use their AF2-generated antibody models as input. The protocol describes the relative advantages of the server compared to other epitope-mapping tools, its limitations and potential areas of improvement. The server may take 45-90 min depending on the size of the proteins.
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What OpenQuestion holds
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.