ArticleNucleic acids research2012
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers, 2 of them syntheses 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
139 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Deciphering the Role of Filamin B Calponin-Homology Domain in Causing the Larsen Syndrome, Boomerang Dysplasia, and Atelosteogenesis Type I Spectrum Disorders via a Computational Approach.Molecules (Basel, Switzerland) · 2020Pooled it
- Angiotensinogen-M235T as a risk factor for myocardial infarction in Asian populations: a genetic association study and a bioinformatics approach.Croatian medical journal · 2016Pooled it
- CD25 expression and outcomes in older patients with acute myelogenous leukemia treated with plerixafor and decitabine.Leukemia & lymphoma · 2018Trial
- A sequence-based classifier distinguishes phenotype-associated genes from other gene models in plants.Genome research · 2026Article
- Genomic analyses of weedy rice reveal historical connections between European and northwestern Chinese rice.Plant communications · 2026Article
- Molecular Modeling of N-Acetylglucosamine Binding to the I154R Mutant of NAGLU: Pathogenic Insights into Sanfilippo Syndrome Type B.International journal of molecular sciences · 2026Article
- Molecular Mechanisms of CLCN5 Missense Mutations in Dent Disease Type 1: A Comprehensive Computational Analysis and Clinical Correlations in a Chinese Cohort.Journal of cellular and molecular medicine · 2026Article
- Diverse reference genomes detect variants in the US winter wheat.The plant genome · 2026Article
- A review on molecular markers ofJournal of parasitic diseases : official organ of the Indian Society for Parasitology · 2025Review
- The first description of CTNNB1 syndrome in the Tunisian population: clinical investigation, molecular docking and molecular dynamics simulation of β-catenin/E-cadherin complex.Molecular biology reports · 2025Article
- Prognostic Modeling of Deleterious IDUA Mutations L238Q and P385R in Hurler Syndrome Through Molecular Dynamics Simulations.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Computational studies on the functional and structural impact of pathogenic mutations in enzymes.Protein science : a publication of the Protein Society · 2025Review
- Genomic variations in Mycobacterium tuberculosis from the lungs and blood of HIV-infected individuals in Uganda: insights into compartmentalization.African health sciences · 2024Article
- Purifying Selection Influences the Comparison of Heterozygosities between Populations.Biology · 2024Article
- Identification of Pathogenic Missense Mutations of NF1 Using Computational Approaches.Journal of molecular neuroscience : MN · 2024Article
- Genomic and phenotypic imprints of microbial domestication on cheese starter cultures.Nature communications · 2024Article
- Characterising the Genomic Landscape of Differentiation Between Annual and Perennial Rye.Evolutionary applications · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- Current status and emerging frontiers in enzyme engineering: An industrial perspective.Heliyon · 2024Review
79 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
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide variants (SNVs) are, together with copy number variation, the primary source of variation in the human genome and are associated with phenotypic variation such as altered response to drug treatment and susceptibility to disease. Linking structural effects of non-synonymous SNVs to functional outcomes is a major issue in structural bioinformatics. The SNPeffect database (http://snpeffect.switchlab.org) uses sequence- and structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins. It integrates aggregation prediction (TANGO), amyloid prediction (WALTZ), chaperone-binding prediction (LIMBO) and protein stability analysis (FoldX) for structural phenotyping. Additionally, SNPeffect holds information on affected catalytic sites and a number of post-translational modifications. The database contains all known human protein variants from UniProt, but users can now also submit custom protein variants for a SNPeffect analysis, including automated structure modeling. The new meta-analysis application allows plotting correlations between phenotypic features for a user-selected set of variants.
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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.