Machine-learning-guided directed evolution for protein engineering

KK Yang, Z Wu, FH Arnold - Nature methods, 2019 - nature.com
Protein engineering through machine-learning-guided directed evolution enables the
optimization of protein functions. Machine-learning approaches predict how sequence maps …

Learning functional properties of proteins with language models

S Unsal, H Atas, M Albayrak, K Turhan… - Nature Machine …, 2022 - nature.com
Data-centric approaches have been used to develop predictive methods for elucidating
uncharacterized properties of proteins; however, studies indicate that these methods should …

Unified rational protein engineering with sequence-based deep representation learning

EC Alley, G Khimulya, S Biswas, M AlQuraishi… - Nature …, 2019 - nature.com
Rational protein engineering requires a holistic understanding of protein function. Here, we
apply deep learning to unlabeled amino-acid sequences to distill the fundamental features …

ProteInfer, deep neural networks for protein functional inference

T Sanderson, ML Bileschi, D Belanger, LJ Colwell - Elife, 2023 - elifesciences.org
Predicting the function of a protein from its amino acid sequence is a long-standing
challenge in bioinformatics. Traditional approaches use sequence alignment to compare a …

Using deep learning to annotate the protein universe

ML Bileschi, D Belanger, DH Bryant, T Sanderson… - Nature …, 2022 - nature.com
Understanding the relationship between amino acid sequence and protein function is a long-
standing challenge with far-reaching scientific and translational implications. State-of-the-art …

ProPythia: A Python package for protein classification based on machine and deep learning

AM Sequeira, D Lousa, M Rocha - Neurocomputing, 2022 - Elsevier
The field of protein data mining has been growing rapidly in the last years. To characterize
proteins and determine their function from their amino acid sequences are challenging and …

Deep learning in biomedical informatics

CL Hung - Intelligent Nanotechnology, 2023 - Elsevier
With the massive influx of multimodal data in the last decade, the role of data analytics in
health informatics has grown rapidly. Deep learning (DL) is defined as a technology based …

Machine learning for protein engineering

KE Johnston, C Fannjiang, BJ Wittmann, BL Hie… - Machine Learning in …, 2023 - Springer
Directed evolution of proteins has been the most effective method for protein engineering.
However, a new paradigm is emerging, fusing the library generation and screening …

ProtEC: A Transformer Based Deep Learning System for Accurate Annotation of Enzyme Commission Numbers

A Tamir, M Salem, JS Yuan - IEEE/ACM Transactions on …, 2023 - ieeexplore.ieee.org
The advancements in next-generation sequencing technologies have given rise to large-
scale, open-source protein databases consisting of hundreds of millions of sequences …

A review of deep learning in computer-aided drug design

CH Chang, CL Hung, CY Tang - 2019 IEEE International …, 2019 - ieeexplore.ieee.org
Recently, Deep Learning has been applied to many medical domains, such as medical
image analysis, bioinformatic, biochemistry, drug design, and so forth, to improve the …