Deep mutational scanning: a new style of protein science
Mutagenesis provides insight into proteins, but only recently have assays that couple
genotype to phenotype been used to assess the activities of as many as 1 million mutant …
genotype to phenotype been used to assess the activities of as many as 1 million mutant …
Scalable functional assays for the interpretation of human genetic variation
Scalable sequence–function studies have enabled the systematic analysis and cataloging of
hundreds of thousands of coding and noncoding genetic variants in the human genome …
hundreds of thousands of coding and noncoding genetic variants in the human genome …
Sequence modeling and design from molecular to genome scale with Evo
The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an
organism's function. We present Evo, a long-context genomic foundation model with a …
organism's function. We present Evo, a long-context genomic foundation model with a …
Proteingym: Large-scale benchmarks for protein fitness prediction and design
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins to address our most pressing …
understanding genetic disease to designing novel proteins to address our most pressing …
An Atlas of Variant Effects to understand the genome at nucleotide resolution
Sequencing has revealed hundreds of millions of human genetic variants, and continued
efforts will only add to this variant avalanche. Insufficient information exists to interpret the …
efforts will only add to this variant avalanche. Insufficient information exists to interpret the …
Predicting and interpreting large-scale mutagenesis data using analyses of protein stability and conservation
Understanding and predicting the functional consequences of single amino acid changes is
central in many areas of protein science. Here, we collect and analyze experimental …
central in many areas of protein science. Here, we collect and analyze experimental …
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …
The spatial architecture of protein function and adaptation
RN McLaughlin Jr, FJ Poelwijk, A Raman, WS Gosal… - Nature, 2012 - nature.com
Statistical analysis of protein evolution suggests a design for natural proteins in which
sparse networks of coevolving amino acids (termed sectors) comprise the essence of three …
sparse networks of coevolving amino acids (termed sectors) comprise the essence of three …
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations
BJ Livesey, JA Marsh - Molecular systems biology, 2020 - embopress.org
To deal with the huge number of novel protein‐coding variants identified by genome and
exome sequencing studies, many computational variant effect predictors (VEPs) have been …
exome sequencing studies, many computational variant effect predictors (VEPs) have been …
Inferring protein 3D structure from deep mutation scans
We describe an experimental method of three-dimensional (3D) structure determination that
exploits the increasing ease of high-throughput mutational scans. Inspired by the success of …
exploits the increasing ease of high-throughput mutational scans. Inspired by the success of …