Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments

M Gantz, S Neun, EJ Medcalf, LD van Vliet… - Chemical …, 2023 - ACS Publications
Novel and improved biocatalysts are increasingly sourced from libraries via experimental
screening. The success of such campaigns is crucially dependent on the number of …

Emerging droplet microfluidics

L Shang, Y Cheng, Y Zhao - Chemical reviews, 2017 - ACS Publications
Droplet microfluidics generates and manipulates discrete droplets through immiscible
multiphase flows inside microchannels. Due to its remarkable advantages, droplet …

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

P Notin, A Kollasch, D Ritter… - Advances in …, 2023 - 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 …

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 …

Self-driving laboratories to autonomously navigate the protein fitness landscape

JT Rapp, BJ Bremer, PA Romero - Nature chemical engineering, 2024 - nature.com
Protein engineering has nearly limitless applications across chemistry, energy and
medicine, but creating new proteins with improved or novel functions remains slow, labor …

Mutation effects predicted from sequence co-variation

TA Hopf, JB Ingraham, FJ Poelwijk, CPI Schärfe… - Nature …, 2017 - nature.com
Many high-throughput experimental technologies have been developed to assess the
effects of large numbers of mutations (variation) on phenotypes. However, designing …

Advances in ultrahigh-throughput screening for directed enzyme evolution

U Markel, KD Essani, V Besirlioglu, J Schiffels… - Chemical Society …, 2020 - pubs.rsc.org
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long
time. In order to exploit their full potential, enzymes often need to be re-engineered or …

Deep generative models of genetic variation capture the effects of mutations

AJ Riesselman, JB Ingraham, DS Marks - Nature methods, 2018 - nature.com
The functions of proteins and RNAs are defined by the collective interactions of many
residues, and yet most statistical models of biological sequences consider sites nearly …

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

D Esposito, J Weile, J Shendure, LM Starita… - Genome biology, 2019 - Springer
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 …

Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning

A Judge, B Sankaran, L Hu, M Palaniappan… - Proceedings of the …, 2024 - pnas.org
Cooperative interactions between amino acids are critical for protein function. A genetic
reflection of cooperativity is epistasis, which is when a change in the amino acid at one …