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Opportunities and challenges for machine learning-assisted enzyme engineering
Enzymes can be engineered at the level of their amino acid sequences to optimize key
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …
Automated in vivo enzyme engineering accelerates biocatalyst optimization
Achieving cost-competitive bio-based processes requires development of stable and
selective biocatalysts. Their realization through in vitro enzyme characterization and …
selective biocatalysts. Their realization through in vitro enzyme characterization and …
Accelerating biocatalysis discovery with machine learning: a paradigm shift in enzyme engineering, discovery, and design
B Markus, K Andreas, K Arkadij, L Stefan, O Gustav… - ACS …, 2023 - ACS Publications
Emerging computational tools promise to revolutionize protein engineering for biocatalytic
applications and accelerate the development timelines previously needed to optimize an …
applications and accelerate the development timelines previously needed to optimize an …
Active learning-assisted directed evolution
Directed evolution (DE) is a powerful tool to optimize protein fitness for a specific application.
However, DE can be inefficient when mutations exhibit non-additive, or epistatic, behavior …
However, DE can be inefficient when mutations exhibit non-additive, or epistatic, behavior …
Evolutionary computation in bioinformatics: A survey
Y Zhang, L Cheng, G Chen, D Alghazzawi - Neurocomputing, 2024 - Elsevier
Bioinformatics is a subject that studies life phenomena by using mathematical and
information science theories and techniques. Its main tasks, such as DNA sequence …
information science theories and techniques. Its main tasks, such as DNA sequence …
A library approach for the de novo high-throughput isolation of humanized VHH domains with favorable developability properties following camelid immunization
P Arras, HB Yoo, L Pekar, C Schröter, T Clarke, S Krah… - MAbs, 2023 - Taylor & Francis
In this study, we generated a novel library approach for high throughput de novo
identification of humanized single-domain antibodies following camelid immunization. To …
identification of humanized single-domain antibodies following camelid immunization. To …
Bayesian optimization in drug discovery
L Colliandre, C Muller - High Performance Computing for Drug Discovery …, 2023 - Springer
Drug discovery deals with the search for initial hits and their optimization toward a targeted
clinical profile. Throughout the discovery pipeline, the candidate profile will evolve, but the …
clinical profile. Throughout the discovery pipeline, the candidate profile will evolve, but the …
AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single …
P Arras, HB Yoo, L Pekar, T Clarke… - Frontiers in Molecular …, 2023 - frontiersin.org
Introduction: In this study, we demonstrate the feasibility of yeast surface display (YSD) and
nextgeneration sequencing (NGS) in combination with artificial intelligence and machine …
nextgeneration sequencing (NGS) in combination with artificial intelligence and machine …
Engineering highly active and diverse nuclease enzymes by combining machine learning and ultra-high-throughput screening
Designing enzymes to function in novel chemical environments is a central goal of synthetic
biology with broad applications. Guiding protein design with machine learning (ML) has the …
biology with broad applications. Guiding protein design with machine learning (ML) has the …
Optimisation strategies for directed evolution without sequencing
J James, S Towers, J Foerster… - PLOS Computational …, 2024 - journals.plos.org
Directed evolution can enable engineering of biological systems with minimal knowledge of
their underlying sequence-to-function relationships. A typical directed evolution process …
their underlying sequence-to-function relationships. A typical directed evolution process …