Design by Directed Evolution

By Frances H. Arnold. 1998

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Citations in the corpus

BERTology Meets Biology: Interpreting Attention in Protein Language Models (2020, background): “Protein science, and especially protein engineering, has historically been driven by experimental, wet-lab methodologies along with biophysical, structure-based intuitions and computational techniques [6, 33, 69].”
ProGen: Language Modeling for Protein Generation (2020, methodology): “In comparison, random mutation, which is the main technique used by state-of-the-art methods such as directed evolution [4] and ML-assisted directed evolution [39], statistically generates samples”
Evolutionary context-integrated deep sequence modeling for protein engineering (2020, background): “Directed evolution is a protein engineering technique that circumvents this intractability in a greedy way [12–14] without the availability of protein structure.”
The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities (2018, neutral): “…connections between surprising results in digital evolution and the products of directed evolution in biology, wherein selection in an experimenter-controlled evolutionary process is manipulated with the hope of improving or adapting proteins or nucleic acids for practical purposes [5, 108].”
Protein sequence design with a learned potential (2020, background): “This range of diverse homologs arise through evolution, where mutations that largely preserve the structure and/or function of proteins can propagate, and impactful experimental methods that mimic evolution have been able to recapitulate this sequence diversity in vitro [30, 31].”
Enzymes for chemical synthesis (2001, background): “Recently, in vitro -directed evolution of enzymes, using random genetic mutation and recombination, followed by screening or selection for a desired trait, has been explored as a more generally applicable approach to the modification of enzyme properties (see the review by Arnold in this issue, ”
Directed evolution converts subtilisin E into a functional equivalent of thermitase. (1999, methodology): “Inspired by natural Darwinian evolution, directed evolution involves mutation, recombination and screening or selection to accumulate the mutations required to achieve significant changes in protein function (Arnold, 1998).”
AdaLead: A simple and robust adaptive greedy search algorithm for sequence design (2020, methodology): “Currently, the most widely used practical approach in sequence design is “directed evolution" (Arnold, 1998), where populations of biological entities are selected through an assay according to their function y , with each iteration becoming more stringent in the selection criteria.”
Guided Generative Protein Design using Regularized Transformers (2022, methodology): “To navigate protein sequence space, researchers have often utilized an iterative search procedure called directed evolution Arnold [1998].”
Model-based reinforcement learning for biological sequence design (2020, background): “The current gold standard for biomolecular design is directed evolution, which was recently recognized with a Nobel prize (Arnold, 1998) and is a form of randomized local search.”