A new age in protein design empowered by deep learning
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 …
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
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 …
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
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 …
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 …
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 …
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 …
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 …
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
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 …
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 …
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 …
processes. Its importance in various applications has led to a growing interest in optimizing …