Navigating the landscape of enzyme design: from molecular simulations to machine learning
J Zhou, M Huang - Chemical Society Reviews, 2024 - pubs.rsc.org
Global environmental issues and sustainable development call for new technologies for fine
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …
xTrimoPGLM: unified 100B-scale pre-trained transformer for deciphering the language of protein
Protein language models have shown remarkable success in learning biological information
from protein sequences. However, most existing models are limited by either autoencoding …
from protein sequences. However, most existing models are limited by either autoencoding …
[HTML][HTML] Data-driven strategies for the computational design of enzyme thermal stability: Trends, perspectives, and prospects: Data-driven strategies for enzyme …
Thermal stability is one of the most important properties of enzymes, which sustains life and
determines the potential for the industrial application of biocatalysts. Although traditional …
determines the potential for the industrial application of biocatalysts. Although traditional …
HybridGCN for protein solubility prediction with adaptive weighting of multiple features
The solubility of proteins stands as a pivotal factor in the realm of pharmaceutical research
and production. Addressing the imperative to enhance production efficiency and curtail …
and production. Addressing the imperative to enhance production efficiency and curtail …
Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline
As genomic databases expand and artificial intelligence tools advance, there is a growing
demand for efficient characterization of large numbers of proteins. To this end, here we …
demand for efficient characterization of large numbers of proteins. To this end, here we …
Deep learning prediction of enzyme optimum pH
The relationship between pH and enzyme catalytic activity, as well as the optimal pH (pHopt)
at which enzymes function, is crucial for biotechnological applications. Consequently …
at which enzymes function, is crucial for biotechnological applications. Consequently …
REME: an integrated platform for reaction enzyme mining and evaluation
Z Shi, D Wang, Y Li, R Deng, J Lin, C Liu… - Nucleic Acids …, 2024 - academic.oup.com
A key challenge in pathway design is finding proper enzymes that can be engineered to
catalyze a non-natural reaction. Although existing tools can identify potential enzymes …
catalyze a non-natural reaction. Although existing tools can identify potential enzymes …
[HTML][HTML] DeepTM: A deep learning algorithm for prediction of melting temperature of thermophilic proteins directly from sequences
M Li, H Wang, Z Yang, L Zhang, Y Zhu - Computational and Structural …, 2023 - Elsevier
Thermally stable proteins find extensive applications in industrial production,
pharmaceutical development, and serve as a highly evolved starting point in protein …
pharmaceutical development, and serve as a highly evolved starting point in protein …
A general temperature-guided language model to engineer enhanced stability and activity in proteins
Designing protein mutants with high stability and activity is a critical yet challenging task in
protein engineering. Here, we introduce PRIME, an innovative deep learning approach for …
protein engineering. Here, we introduce PRIME, an innovative deep learning approach for …
Recent Advances in the Integration of Protein Mechanics and Machine Learning
Mechanics underlies protein properties and behavior. From a theoretical standpoint, it is
possible to derive these based on physical rules. This is appealing because they provide …
possible to derive these based on physical rules. This is appealing because they provide …