A new age in protein design empowered by deep learning

H Khakzad, I Igashov, A Schneuing, C Goverde… - Cell Systems, 2023 - cell.com
The rapid progress in the field of deep learning has had a significant impact on protein
design. Deep learning methods have recently produced a breakthrough in protein structure …

AlphaFold2 and deep learning for elucidating enzyme conformational flexibility and its application for design

G Casadevall, C Duran, S Osuna - JACS Au, 2023 - ACS Publications
The recent success of AlphaFold2 (AF2) and other deep learning (DL) tools in accurately
predicting the folded three-dimensional (3D) structure of proteins and enzymes has …

Advancing enzyme's stability and catalytic efficiency through synergy of force-field calculations, evolutionary analysis, and machine learning

A Kunka, SM Marques, M Havlasek, M Vasina… - ACS …, 2023 - ACS Publications
Thermostability is an essential requirement for the use of enzymes in the bioindustry. Here,
we compare different protein stabilization strategies using a challenging target, a stable …

High-Throughput Screening Techniques for the Selection of Thermostable Enzymes

L Li, X Liu, Y Bai, B Yao, H Luo, T Tu - Journal of Agricultural and …, 2024 - ACS Publications
The acquisition of a thermostable enzyme is an indispensable prerequisite for its successful
implementation in industrial applications and the development of novel functionalities …

Solvatochromic sensors detect proteome aggregation in stressed liver tissues with hepatic cancer and cirrhosis

B Jing, J Li, K Guo, L Zeng, J Sui, Z Zhang… - Journal of Materials …, 2023 - pubs.rsc.org
Protein misfolding and aggregation involve complex cellular processes with clinical
implications in various diseases. However, the detection of aggregated proteomes without …

Metalloenzyme-inspired approach to the design and applications of phosphatase-mimetic nanozymes. Bridging the inorganic and organic worlds

P Janoš - Environmental Science: Nano, 2024 - pubs.rsc.org
Nanozymes were introduced approximately 15 years ago as inorganic materials capable of
mimicking the catalytic abilities of natural (protein-based) enzymes. While the catalytic …

In Vitro Biotransformation of High-Titer d-Glucarate by Stepwise-Added Enzyme Cocktails

Y Li, C You, YHPJ Zhang - Organic Process Research & …, 2024 - ACS Publications
d-Glucaric acid (GA), one of the polyhydroxy dicarboxylic acids, is known for its great
potentials in the polymer, food, detergent, and pharmaceutical industries. Here, we …

ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers

Q Tan, J Xiao, J Chen, Y Wang, Z Zhang… - Briefings in …, 2024 - academic.oup.com
Accurate understanding of the biological functions of enzymes is vital for various tasks in
both pathologies and industrial biotechnology. However, the existing methods are usually …

Classifying protein kinase conformations with machine learning

I Reveguk, T Simonson - Protein Science, 2024 - Wiley Online Library
Protein kinases are key actors of signaling networks and important drug targets. They cycle
between active and inactive conformations, distinguished by a few elements within the …

Multiple Cofactor Engineering Strategies to Enhance Pyridoxine Production in Escherichia coli

L Wu, J Li, Y Zhang, Z Tian, Z Jin, L Liu, D Zhang - Microorganisms, 2024 - mdpi.com
Pyridoxine, also known as vitamin B6, is an essential cofactor in numerous cellular
processes. Its importance in various applications has led to a growing interest in optimizing …