ArticleProteins2014
Evaluation of predictions in the CASP10 model refinement category.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 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
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Who cites it
63 citing papers in PubMed.
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- Immunoinformatic Prediction of HIV-1 Glycoprotein gp120 and Nef Epitopes Conjugated to HBsAg-Binding Protein (SBP) to Induce the Humoral and Cellular Immune Response.International journal of molecular sciences · 2025Article
- An outlook on structural biology after AlphaFold: tools, limits and perspectives.FEBS open bio · 2025Review
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- Considerations on Structural Vaccinology and Epitope Screening of Calcium-Dependent Protein Kinases 8 as a Potential Vaccine Target AgainstInterdisciplinary perspectives on infectious diseases · 2025Article
- Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration.MethodsX · 2024Article
- Immunoinformatic Identification of Multiple Epitopes of gp120 Protein of HIV-1 to Enhance the Immune Response against HIV-1 Infection.International journal of molecular sciences · 2024Article
- A computational approach to design a polyvalent vaccine against human respiratory syncytial virus.Scientific reports · 2023Article
- Immunoinformatics-guided designing and in silico analysis of epitope-based polyvalent vaccines against multiple strains of human coronavirus (HCoV).Expert review of vaccines · 2022Article
- Immunoinformatics Approach to Design Novel Subunit Vaccine against the Epstein-Barr Virus.Microbiology spectrum · 2022Article
- Core Proteomics and Immunoinformatic Approaches to Design a Multiepitope Reverse Vaccine Candidate against Chagas Disease.Vaccines · 2022Article
- Immunoinformatics Studies and Design of a Potential Multi-Epitope Peptide Vaccine to Combat the Fatal Visceral Leishmaniasis.Vaccines · 2022Article
- Application of reverse vaccinology to design a multi-epitope subunit vaccine against a new strain of Aeromonas veronii.Journal, genetic engineering & biotechnology · 2022Article
- Structure-conditioned amino-acid couplings: How contact geometry affects pairwise sequence preferences.Protein science : a publication of the Protein Society · 2022Article
- Designing a novel mRNA vaccine against Vibrio harveyi infection in fish: an immunoinformatics approach.Genomics & informatics · 2022Article
- Immunoinformatic Design of a Multivalent Peptide Vaccine Against Mucormycosis: Targeting FTR1 Protein of Major Causative Fungi.Frontiers in immunology · 2022Article
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- Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics.Biochemistry and biophysics reports · 2021Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Here we report on the assessment results of the third experiment to evaluate the state of the art in protein model refinement, where participants were invited to improve the accuracy of initial protein models for 27 targets. Using an array of complementary evaluation measures, we find that five groups performed better than the naïve (null) method-a marked improvement over CASP9, although only three were significantly better. The leading groups also demonstrated the ability to consistently improve both backbone and side chain positioning, while other groups reliably enhanced other aspects of protein physicality. The top-ranked group succeeded in improving the backbone conformation in almost 90% of targets, suggesting a strategy that for the first time in CASP refinement is successful in a clear majority of cases. A number of issues remain unsolved: the majority of groups still fail to improve the quality of the starting models; even successful groups are only able to make modest improvements; and no prediction is more similar to the native structure than to the starting model. Successful refinement attempts also often go unrecognized, as suggested by the relatively larger improvements when predictions not submitted as model 1 are also considered.
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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.