ArticleJournal of molecular biology2019
PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants.
Article in Journal of molecular biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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.
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Who cites it
16 citing papers in PubMed.
- Genomic landscape of drug binding and pharmacogenetic variation across diverse populations using SNPdrug3D.Nature communications · 2026Article
- Review
- ProtVar: mapping and contextualizing human missense variation.Nucleic acids research · 2024Article
- 3DVizSNP: a tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D.BMC bioinformatics · 2023Article
- Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data.Scientific data · 2023Article
- Delineation of functionally essential protein regions for 242 neurodevelopmental genes.Brain : a journal of neurology · 2023Article
- Assessing the Pathogenicity of In-Frame CACNA1F Indel Variants Using Structural Modeling.The Journal of molecular diagnostics : JMD · 2022Article
- GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes.Journal of molecular biology · 2022Article
- PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow.Journal of cheminformatics · 2022Article
- A variant inMeta gene · 2021Article
- Missense3D-DB web catalogue: an atom-based analysis and repository of 4M human protein-coding genetic variants.Human genetics · 2021Article
- SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability.International journal of molecular sciences · 2021Article
- Mapping OMIM Disease-Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes.Frontiers in molecular biosciences · 2021Article
- MISCAST: MIssense variant to protein StruCture Analysis web SuiTe.Nucleic acids research · 2020Article
- VarSite: Disease variants and protein structure.Protein science : a publication of the Protein Society · 2020Article
- MoMI-G: modular multi-scale integrated genome graph browser.BMC bioinformatics · 2019Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
PhyreRisk is an open-access, publicly accessible web application for interactively bridging genomic, proteomic and structural data facilitating the mapping of human variants onto protein structures. A major advance over other tools for sequence-structure variant mapping is that PhyreRisk provides information on 20,214 human canonical proteins and an additional 22,271 alternative protein sequences (isoforms). Specifically, PhyreRisk provides structural coverage (partial or complete) for 70% (14,035 of 20,214 canonical proteins) of the human proteome, by storing 18,874 experimental structures and 84,818 pre-built models of canonical proteins and their isoforms generated using our in house Phyre2. PhyreRisk reports 55,732 experimentally, multi-validated protein interactions from IntAct and 24,260 experimental structures of protein complexes. Another major feature of PhyreRisk is that, rather than presenting a limited set of precomputed variant-structure mapping of known genetic variants, it allows the user to explore novel variants using, as input, genomic coordinates formats (Ensembl, VCF, reference SNP ID and HGVS notations) and Human Build GRCh37 and GRCh38. PhyreRisk also supports mapping variants using amino acid coordinates and searching for genes or proteins of interest. PhyreRisk is designed to empower researchers to translate genetic data into protein structural information, thereby providing a more comprehensive appreciation of the functional impact of variants. PhyreRisk is freely available at http://phyrerisk.bc.ic.ac.uk.
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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.