ArticleJournal of molecular biology2023
Missense3D-PPI: A Web Resource to Predict the Impact of Missense Variants at Protein Interfaces Using 3D Structural Data.
Article in Journal of molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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
17 citing papers in PubMed.
- 3DSeqCheck: A Web-based Tool for Verifying Sequence Consistency Between a 3D Structure File and the Corresponding UniProt Entry.Journal of molecular biology · 2026Article
- Metabolomics profiling reveals changes in peptidoglycan and redox metabolism between ancient and modernMicrobiology spectrum · 2026Article
- CATVariant: a web server for integrated protein variant interpretation across sequence, structure, population, and clinical evidence.Nucleic acids research · 2026Article
- Advancing risk gene discovery across the allele frequency spectrum.HGG advances · 2026Review
- Conserved histidine residues and the control of tick-borne encephalitis virus maturation.The Journal of general virology · 2026Article
- Novel Genotype-Phenotype Correlations inOphthalmology science · 2026Article
- Computational screening of oncogenic genetic variations in tumor suppressor proteins driving gastric cancer pathogenesis.PloS one · 2026Article
- Article
- Accurate identification and mechanistic evaluation of pathogenic missense variants withProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Discovery of a NovelMolecular syndromology · 2025Article
- Expanding the Clinical Spectrum ofInternational journal of molecular sciences · 2025Article
- DS-MVP: identifying disease-specific pathogenicity of missense variants by pre-training representation.Briefings in bioinformatics · 2025Article
- Tumor-Agnostic Therapies in Practice: Challenges, Innovations, and Future Perspectives.Cancers · 2025Review
- Unraveling the impact ofIn silico pharmacology · 2025Article
- Nuclear-Cytoplasmic Shuttling of the Usher Syndrome 1G Protein SANS Differs from Its Paralog ANKS4B.Cells · 2024Article
- Landscape of FLT3 Variations Associated with Structural and Functional Impact on Acute Myeloid Leukemia: A Computational Study.International journal of molecular sciences · 2024Article
- Missense3D-TM: Predicting the Effect of Missense Variants in Helical Transmembrane Protein Regions Using 3D Protein Structures.Journal of molecular biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
In 2019, we released Missense3D which identifies stereochemical features that are disrupted by a missense variant, such as introducing a buried charge. Missense3D analyses the effect of a missense variant on a single structure and thus may fail to identify as damaging surface variants disrupting a protein interface i.e., a protein-protein interaction (PPI) site. Here we present Missense3D-PPI designed to predict missense variants at PPI interfaces. Our development dataset comprised of 1,279 missense variants (pathogenic n = 733, benign n = 546) in 434 proteins and 545 experimental structures of PPI complexes. Benchmarking of Missense3D-PPI was performed after dividing the dataset in training (320 benign and 320 pathogenic variants) and testing (226 benign and 413 pathogenic). Structural features affecting PPI, such as disruption of interchain bonds and introduction of unbalanced charged interface residues, were analysed to assess the impact of the variant at PPI. The performance of Missense3D-PPI was superior to that of Missense3D: sensitivity 44 % versus 8% and accuracy 58% versus 40%, p = 4.23 × 10
Indexed as
Identifiers
What Socratic 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 Socratic graph.