ArticleBMC bioinformatics2013
Bioinformatics analysis of the epitope regions for norovirus capsid protein.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 93 citations in OpenAlex.
- Elucidation of Increased Cervical Cancer Risk Due to Polymorphisms in XRCC1 (R399Q and R194W), ERCC5 (D1104H), and NQO1 (P187S).Reproductive sciences (Thousand Oaks, Calif.) · 2023Pooled it
- Insilico Analysis of CYP17A1 in the Pathogenesis of Polycystic Ovarian Syndrome by Molecular Dynamics and Genotypic Characterization.Reproductive sciences (Thousand Oaks, Calif.) · 2026Article
- The co-occurrence of homozygous variants in GUCY2D and MYO7A in Leber congenital amaurosis associated with deafness: clinical, molecular, and in silico investigation.Molecular biology reports · 2026Article
- Predicting high-risk clinical missense variants of SMARCB1 in rare neurogenetic disorder schwannomatosis (nerve tumor) through sequence, structure, and molecular dynamics analyses.Neurogenetics · 2025Article
- Elucidating the functional impact of G137V and G144R variants in Maroteaux Lamy's Syndrome by Molecular Dynamics Simulation.Molecular diversity · 2024Article
- Pathogenic missense variation in PABPC1L/EPAB causes female infertility due to oocyte maturation arrest at the germinal vesicle stage.Journal of assisted reproduction and genetics · 2024Article
- Review
- Immunoinformatics-aided design of a new multi-epitope vaccine adjuvanted with domain 4 of pneumolysin against Streptococcus pneumoniae strains.BMC bioinformatics · 2023Article
- Combined in Silico Prediction Methods, Molecular Dynamic Simulation, and Molecular Docking of FOXG1 Missense Mutations: Effect on FoxG1 Structure and Its Interactions with DNA and Bmi-1 Protein.Journal of molecular neuroscience : MN · 2022Article
- Recombination of Single Beneficial Substitutions Obtained from Protein Engineering by Computer-Assisted Recombination (CompassR).Methods in molecular biology (Clifton, N.J.) · 2022Article
- Molecular dynamics, residue network analysis, and cross-correlation matrix to characterize the deleterious missense mutations in GALE causing galactosemia III.Cell biochemistry and biophysics · 2021Article
- Molecular evolution of the capsid gene in human norovirus genogroup II.Scientific reports · 2016Article
- Molecular Evolution of the Capsid Gene in Norovirus Genogroup I.Scientific reports · 2015Article
- Norovirus.Clinical microbiology reviews · 2015Review
- Norovirus in healthcare settings.Current opinion in infectious diseases · 2014Review
- Molecular epidemiology of genogroup II noroviruses infection in outpatients with acute gastroenteritis in Nanjing, China (2010-2013).BioMed research international · 2014Article
- Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4.Bioinformation · 2013Article
- Computational vaccinology and the ICoVax 2012 workshop.BMC bioinformatics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNorovirus is the major cause of nonbacterial epidemic gastroenteritis, being highly prevalent in both developing and developed countries. Despite of the available monoclonal antibodies (MAbs) for different sub-genogroups, a comprehensive epitope analysis based on various bioinformatics technology is highly desired for future potential antibody development in clinical diagonosis and treatment.
methodsA total of 18 full-length human norovirus capsid protein sequences were downloaded from GenBank. Protein modeling was performed with program Modeller 9.9. The modeled 3D structures of capsid protein of norovirus were submitted to the protein antigen spatial epitope prediction webserver (SEPPA) for predicting the possible spatial epitopes with the default threshold. The results were processed using the Biosoftware.
resultsCompared with GI, we found that the GII genogroup had four deletions and two special insertions in the VP1 region. The predicted conformational epitope regions mainly concentrated on N-terminal (1~96), Middle Part (298~305, 355~375) and C-terminal (560~570). We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup.
conclusionsThe predicted conformational epitope regions of norovirus VP1 mainly concentrated on N-terminal, Middle Part and C-terminal. We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup. The overlapping with experimental epitopes indicates the important role of latest computational technologies. With the fast development of computational immunology tools, the bioinformatics pipeline will be more and more critical to vaccine design.
Indexed as
Identifiers
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.