Protein engineering, design & selection : PEDS
Jan 29, 2024
Sequence design is a crucial step in the process of designing or engineering proteins. Traditionally, physics-based methods have been used to solve for optimal sequences, with the main disadvantages being that they are computationally intensive for t...
Protein engineering, design & selection : PEDS
Jan 29, 2024
Deep learning methods for protein sequence design focus on modeling and sampling the many- dimensional distribution of amino acid sequences conditioned on the backbone structure. To produce physically foldable sequences, inter-residue couplings need ...
Protein engineering, design & selection : PEDS
Jan 21, 2023
Numerous cellular functions rely on protein-protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep learning has emerged as a...
Protein engineering, design & selection : PEDS
Jan 21, 2023
Identifying function-enhancing enzyme variants is a 'holy grail' challenge in protein science because it will allow researchers to expand the biocatalytic toolbox for late-stage functionalization of drug-like molecules, environmental degradation of p...
Protein engineering, design & selection : PEDS
Feb 15, 2021
Machine learning is a useful computational tool for large and complex tasks such as those in the field of enzyme engineering, selection and design. In this review, we examine enzyme-related applications of machine learning. We start by comparing tool...