Epistasis and adaptation on fitness landscapes

C Bank - Annual Review of Ecology, Evolution, and Systematics, 2022 - annualreviews.org
Epistasis occurs when the effect of a mutation depends on its carrier's genetic background.
Despite increasing evidence that epistasis for fitness is common, its role during evolution is …

The causes and consequences of genetic interactions (epistasis)

J Domingo, P Baeza-Centurion… - Annual review of …, 2019 - annualreviews.org
The same mutation can have different effects in different individuals. One important reason
for this is that the outcome of a mutation can depend on the genetic context in which it …

Language models enable zero-shot prediction of the effects of mutations on protein function

J Meier, R Rao, R Verkuil, J Liu… - Advances in neural …, 2021 - proceedings.neurips.cc
Modeling the effect of sequence variation on function is a fundamental problem for
understanding and designing proteins. Since evolution encodes information about function …

Proteingym: Large-scale benchmarks for protein fitness prediction and design

P Notin, A Kollasch, D Ritter… - Advances in …, 2024 - proceedings.neurips.cc
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 …

Protein design and variant prediction using autoregressive generative models

JE Shin, AJ Riesselman, AW Kollasch… - Nature …, 2021 - nature.com
The ability to design functional sequences and predict effects of variation is central to protein
engineering and biotherapeutics. State-of-art computational methods rely on models that …

Epistatic drift causes gradual decay of predictability in protein evolution

Y Park, BPH Metzger, JW Thornton - Science, 2022 - science.org
Epistatic interactions can make the outcomes of evolution unpredictable, but no
comprehensive data are available on the extent and temporal dynamics of changes in the …

A combinatorially complete epistatic fitness landscape in an enzyme active site

KE Johnston, PJ Almhjell, EJ Watkins-Dulaney… - Proceedings of the …, 2024 - pnas.org
Protein engineering often targets binding pockets or active sites which are enriched in
epistasis—nonadditive interactions between amino acid substitutions—and where the …

The simplicity of protein sequence-function relationships

Y Park, BPH Metzger, JW Thornton - Nature Communications, 2024 - nature.com
How complex are the rules by which a protein's sequence determines its function? High-
order epistatic interactions among residues are thought to be pervasive, suggesting an …

Molecular determinants of protein evolvability

K Buda, CM Miton, XC Fan, N Tokuriki - Trends in Biochemical Sciences, 2023 - cell.com
The plethora of biological functions that sustain life is rooted in the remarkable evolvability of
proteins. An emerging view highlights the importance of a protein's initial state in dictating …

Idiosyncratic epistasis leads to global fitness–correlated trends

CW Bakerlee, AN Nguyen Ba, Y Shulgina… - Science, 2022 - science.org
Epistasis can markedly affect evolutionary trajectories. In recent decades, protein-level
fitness landscapes have revealed extensive idiosyncratic epistasis among specific …