ArticleBiophysical journal2019
Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking.
Article in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- The prevalence of protein misfolding as a mechanism for hereditary deafness.PLoS genetics · 2026Article
- Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.The Journal of chemical physics · 2024Article
- Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome.Human genetics · 2023Article
- Assessing Variants of Uncertain Significance Implicated in Hearing Loss Using a Comprehensive Deafness Proteome.Research square · 2023Article
- Germline landscape ofFrontiers in oncology · 2023Article
- Whole-genome sequencing reveals de-novo mutations associated with nonsyndromic cleft lip/palate.Scientific reports · 2022Article
- In Silico and In Vivo Analysis of Amino Acid Substitutions That Cause Laminopathies.International journal of molecular sciences · 2021Article
- Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.Journal of chemical theory and computation · 2021Article
- Nanophthalmos patient with a THR518MET mutation in MYRF, a case report.BMC ophthalmology · 2020Article
- Characterization of a TP53 Somatic Variant of Unknown Function From an Ovarian Cancer Patient Using Organoid Culture and Computational Modeling.Clinical obstetrics and gynecology · 2020Article
- Long-Term Follow-Up on a Juvenile Open-Angle Glaucoma Pedigree with a Novel EFEMP1 Mutation (c.1313, p.Tyr438Cys).Ophthalmology. GlaucomaArticle
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
Abstract
Hearing loss is associated with ∼8100 mutations in 152 genes, and within the coding regions of these genes are over 60,000 missense variants. The majority of these variants are classified as "variants of uncertain significance" to reflect our inability to ascribe a phenotypic effect to the observed amino acid change. A promising source of pathogenicity information is biophysical simulation, although input protein structures often contain defects because of limitations in experimental data and/or only distant homology to a template. Here, we combine the polarizable atomic multipole optimized energetics for biomolecular applications force field, many-body optimization theory, and graphical processing unit acceleration to repack all deafness-associated proteins and thereby improve average structure MolProbity score from 2.2 to 1.0. We then used these optimized wild-type models to create over 60,000 structures for missense variants in the Deafness Variation Database, which are being incorporated into the Deafness Variation Database to inform deafness pathogenicity prediction. Finally, this work demonstrates that advanced polarizable atomic multipole force fields are efficient enough to repack the entire human proteome.
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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.