[HTML][HTML] Can predicted protein 3D structures provide reliable insights into whether missense variants are disease associated?

S Ittisoponpisan, SA Islam, T Khanna, E Alhuzimi… - Journal of molecular …, 2019 - Elsevier
Abstract Knowledge of protein structure can be used to predict the phenotypic consequence
of a missense variant. Since structural coverage of the human proteome can be roughly …

Interpretation of cancer mutations using a multiscale map of protein systems

F Zheng, MR Kelly, DJ Ramms, ML Heintschel, K Tao… - Science, 2021 - science.org
INTRODUCTION Tumor genome sequencing has revealed that, beyond a few commonly
mutated genes, most mutations that affect cancer genomes are rare. To interpret these rare …

Proximity-dependent biotinylation mediated by TurboID to identify protein–protein interaction networks in yeast

M Larochelle, D Bergeron, B Arcand… - Journal of cell …, 2019 - journals.biologists.com
The use of proximity-dependent biotinylation assays coupled to mass spectrometry (PDB-
MS) has changed the field of protein–protein interaction studies. However, despite the …

Disruption of protein function by pathogenic mutations: common and uncommon mechanisms

M Taipale - Biochemistry and Cell Biology, 2019 - cdnsciencepub.com
Mutations in protein-coding regions underlie almost all Mendelian disorders, drive
tumorigenesis, and contribute to susceptibility to common diseases. Despite the great …

MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles

M Tiberti, T Terkelsen, K Degn, L Beltrame… - Briefings in …, 2022 - academic.oup.com
Mutations, which result in amino acid substitutions, influence the stability of proteins and
their binding to biomolecules. A molecular understanding of the effects of protein mutations …

Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants

A Laddach, JCF Ng, F Fraternali - PLoS Biology, 2021 - journals.plos.org
Missense variants are present amongst the healthy population, but some of them are
causative of human diseases. A classification of variants associated with “healthy” or …

A phage-assisted continuous selection approach for deep mutational scanning of protein–protein interactions

J Zinkus-Boltz, C DeValk, BC Dickinson - ACS Chemical Biology, 2019 - ACS Publications
Protein–protein interactions (PPIs) are critical for organizing molecules in a cell and
mediating signaling pathways. Dysregulation of PPIs is often a key driver of disease. To …

[HTML][HTML] Variational kinetic clustering of complex networks

V Koskin, A Kells, J Clayton, AK Hartmann… - The Journal of …, 2023 - pubs.aip.org
Efficiently identifying the most important communities and key transition nodes in weighted
and unweighted networks is a prevalent problem in a wide range of disciplines. Here, we …

In proteins, the structural responses of a position to mutation rely on the Goldilocks principle: not too many links, not too few

R Dorantes-Gilardi, L Bourgeat, L Pacini… - Physical Chemistry …, 2018 - pubs.rsc.org
A disease has distinct genetic and molecular hallmarks such as sequence variants that are
likely to produce the alternative protein structures accountable for individual responses to …

The identification of childhood asthma progression-related lncRNAs and mRNAs suitable as biomarkers using weighted gene coexpression network analysis

M Hao, J Zan, HI Ahmad - Genetics research, 2021 - cambridge.org
Background. Asthma is a common chronic respiratory disease in children, seriously affecting
children's health and growth. This bioinformatics study aimed to identify potential RNA …