Predicting Drug Resistance Using Deep Mutational Scanning [PDF]
Molecules, 2020 Drug resistance is a major healthcare challenge, resulting in a continuous need to develop new inhibitors. The development of these inhibitors requires an understanding of the mechanisms of resistance for a critical mass of occurrences.
Gur Pines +2 more
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phydms: software for phylogenetic analyses informed by deep mutational scanning [PDF]
PeerJ, 2017 It has recently become possible to experimentally measure the effects of all amino-acid point mutations to proteins using deep mutational scanning.
Sarah K. Hilton +2 more
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A statistical framework for analyzing deep mutational scanning data
Genome Biology, 2017 Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational scanning statistical model that generates error estimates for each measurement, capturing both ...
Alan F. Rubin +6 more
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Deep Mutational Scanning of Viral Glycoproteins and Their Host Receptors [PDF]
Frontiers in Molecular Biosciences, 2021 Deep mutational scanning or deep mutagenesis is a powerful tool for understanding the sequence diversity available to viruses for adaptation in a laboratory setting.
Krishna K. Narayanan, Erik Procko
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Optimization of the antimicrobial peptide Bac7 by deep mutational scanning
BMC Biology, 2022 Background Intracellularly active antimicrobial peptides are promising candidates for the development of antibiotics for human applications. However, drug development using peptides is challenging as, owing to their large size, an enormous sequence space
Philipp Koch +9 more
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Updated benchmarking of variant effect predictors using deep mutational scanning
Molecular Systems Biology, 2023 The assessment of variant effect predictor (VEP) performance is fraught with biases introduced by benchmarking against clinical observations. In this study, building on our previous work, we use independently generated measurements of protein function ...
Benjamin J Livesey, Joseph A Marsh
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Variant effect predictions capture some aspects of deep mutational scanning experiments [PDF]
BMC Bioinformatics, 2020 Background Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, or non ...
Jonas Reeb, Theresa Wirth, Burkhard Rost
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Elucidating the Molecular Determinants of Aβ Aggregation with Deep Mutational Scanning [PDF]
G3: Genes, Genomes, Genetics, 2019 Despite the importance of Aβ aggregation in Alzheimer’s disease etiology, our understanding of the sequence determinants of aggregation is sparse and largely derived from in vitro studies. For example, in vitro proline and alanine scanning mutagenesis of
Vanessa E. Gray +6 more
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popDMS infers mutation effects from deep mutational scanning data. [PDF]
BioinformaticsAbstract Summary Deep mutational scanning (DMS) experiments provide a powerful method to measure the functional effects of genetic mutations at massive scales. However, the data generated from these experiments can be difficult to analyze, with significant variation between experimental replicates. To
Hong Z, Shimagaki KS, Barton JP.
europepmc +7 more sources
Deep mutational scanning of essential bacterial proteins can guide antibiotic development
Nature Communications, 2023 Deep mutational scanning can be used to investigate protein function and stability. Here, Dewachter et al. use deep mutational scanning on three essential bacterial proteins to study the mutations’ effects in their original genomic context, providing ...
Liselot Dewachter +9 more
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