Literature DB >> 33647531

Advances in machine learning for directed evolution.

Bruce J Wittmann1, Kadina E Johnston1, Zachary Wu2, Frances H Arnold3.   

Abstract

Machine learning (ML) can expedite directed evolution by allowing researchers to move expensive experimental screens in silico. Gathering sequence-function data for training ML models, however, can still be costly. In contrast, raw protein sequence data is widely available. Recent advances in ML approaches use protein sequences to augment limited sequence-function data for directed evolution. We highlight contributions in a growing effort to use sequences to reduce or eliminate the amount of sequence-function data needed for effective in silico screening. We also highlight approaches that use ML models trained on sequences to generate new functional sequence diversity, focusing on strategies that use these generative models to efficiently explore vast regions of protein space.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Year:  2021        PMID: 33647531     DOI: 10.1016/j.sbi.2021.01.008

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  10 in total

Review 1.  Learning Strategies in Protein Directed Evolution.

Authors:  Xavier F Cadet; Jean Christophe Gelly; Aster van Noord; Frédéric Cadet; Carlos G Acevedo-Rocha
Journal:  Methods Mol Biol       Date:  2022

2.  Cluster learning-assisted directed evolution.

Authors:  Yuchi Qiu; Jian Hu; Guo-Wei Wei
Journal:  Nat Comput Sci       Date:  2021-12-09

3.  A versatile active learning workflow for optimization of genetic and metabolic networks.

Authors:  Amir Pandi; Christoph Diehl; Ali Yazdizadeh Kharrazi; Scott A Scholz; Elizaveta Bobkova; Léon Faure; Maren Nattermann; David Adam; Nils Chapin; Yeganeh Foroughijabbari; Charles Moritz; Nicole Paczia; Niña Socorro Cortina; Jean-Loup Faulon; Tobias J Erb
Journal:  Nat Commun       Date:  2022-07-05       Impact factor: 17.694

4.  In silico evolution of nucleic acid-binding proteins from a nonfunctional scaffold.

Authors:  Samuel A Raven; Blake Payne; Mitchell Bruce; Aleksandra Filipovska; Oliver Rackham
Journal:  Nat Chem Biol       Date:  2022-02-24       Impact factor: 16.174

Review 5.  Machine learning to navigate fitness landscapes for protein engineering.

Authors:  Chase R Freschlin; Sarah A Fahlberg; Philip A Romero
Journal:  Curr Opin Biotechnol       Date:  2022-04-09       Impact factor: 10.279

Review 6.  Recent Advances in Biocatalysis for Drug Synthesis.

Authors:  Alina Kinner; Philipp Nerke; Regine Siedentop; Till Steinmetz; Thomas Classen; Katrin Rosenthal; Markus Nett; Jörg Pietruszka; Stephan Lütz
Journal:  Biomedicines       Date:  2022-04-21

7.  SYNBIP: synthetic binding proteins for research, diagnosis and therapy.

Authors:  Xiaona Wang; Fengcheng Li; Wenqi Qiu; Binbin Xu; Yanlin Li; Xichen Lian; Hongyan Yu; Zhao Zhang; Jianxin Wang; Zhaorong Li; Weiwei Xue; Feng Zhu
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

Review 8.  Intelligent host engineering for metabolic flux optimisation in biotechnology.

Authors:  Lachlan J Munro; Douglas B Kell
Journal:  Biochem J       Date:  2021-10-29       Impact factor: 3.857

Review 9.  Current state of and need for enzyme engineering of 2-deoxy-D-ribose 5-phosphate aldolases and its impact.

Authors:  Juha Rouvinen; Martina Andberg; Johan Pääkkönen; Nina Hakulinen; Anu Koivula
Journal:  Appl Microbiol Biotechnol       Date:  2021-08-19       Impact factor: 4.813

10.  Generalized Property-Based Encoders and Digital Signal Processing Facilitate Predictive Tasks in Protein Engineering.

Authors:  David Medina-Ortiz; Sebastian Contreras; Juan Amado-Hinojosa; Jorge Torres-Almonacid; Juan A Asenjo; Marcelo Navarrete; Álvaro Olivera-Nappa
Journal:  Front Mol Biosci       Date:  2022-07-14
  10 in total

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