Machine learning (ML) methods have emerged as an efficient surrogate for high-level electronic structure theory, offering precision and computational efficiency. However, the vast conformational and chemical space remains challenging when constructing a general force field. Training data sets typically cover only a limited region of this space, resulting in poor extrapolation performance. Traditional strategies must address this problem by training models from scratch using old and new data sets. In addition, model transferability is crucial for general force field construction. Existing ML force fields, designed for closed systems with no external environmental potential, exhibit limited transferability to complex condensed phase systems such as enzymatic reactions, resulting in inferior performance and high memory costs. Our ML/MM model, based on the Taylor expansion of the electrostatic operator, showed high transferability between reactions in several simple solvents. This work extends the strategy to enzymatic reactions to explore the transferability between more complex heterogeneous environments. In addition, we also apply continual learning strategies based on memory data sets to enable autonomous and on-the-fly training on a continuous stream of new data. By combining these two methods, we can efficiently construct a force field that can be applied to chemical reactions in various environmental media.
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http://dx.doi.org/10.1021/acs.jctc.4c01393 | DOI Listing |
J Chem Theory Comput
March 2025
Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
Machine learning (ML) methods have emerged as an efficient surrogate for high-level electronic structure theory, offering precision and computational efficiency. However, the vast conformational and chemical space remains challenging when constructing a general force field. Training data sets typically cover only a limited region of this space, resulting in poor extrapolation performance.
View Article and Find Full Text PDFChembiochem
March 2025
Colorado School of Mines, Chemistry, 1500 Illinois St, 80403, Golden, UNITED STATES OF AMERICA.
We present the synthesis, properties, and imaging applications of a new class of diazaborine-based probes (Peroxynitrite Probe-1, PNP-1) for selective peroxynitrite (ONOO-) imaging in live cells. PNP-1 features a diazaborine-based reaction motif that provides excellent discrimination between H2O2 and ONOO-, solving a persistent challenge of organoboron-based fluorescent probes for oxidative metabolite imaging. We demonstrate the utility of PNP-1 to detect endogenously produced ONOO- in live RAW 264.
View Article and Find Full Text PDFInt J Biol Macromol
March 2025
State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China. Electronic address:
Alkaline protease has been commercially used in the areas of detergents, food and agriculture, and improving the performance and production of alkaline protease serves as an important role in promoting its market expansion. Here, an alkaline protease AE0 from Alkalihalobacillus clausii FYX was firstly characterized in Bacillus licheniformis DW2△aprE, the optimal temperature and pH of AE0 were 60 °C and 10.5, the K and K values for casein were 17.
View Article and Find Full Text PDFPLoS One
March 2025
Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
Ovarian cancer therapy remains a challenge for human health, partly due to chemotherapy resistance. Understanding the molecular mechanisms underlying this resistance is crucial. Therefore, to identify genes involved in cisplatin resistance in ovarian cancer, RNA-seq analysis of A2780cp (cisplatin-resistant) and A2780 (cisplatin-sensitive) cell lines was performed, revealing 1-acylglycerol-3-phosphate O-acyltransferase 3 (AGPAT3) as a differentially expressed candidate gene.
View Article and Find Full Text PDFACS Omega
March 2025
Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand.
Enzyme-based biosensors have emerged as an effective alternative, providing simplicity, high sensitivity, and the capability to detect multiple residues. However, despite their widespread use, limited studies have examined how organic solvents inhibit these sensors. This study investigates the enzymatic reactions and structure of the selected model enzyme, papain, a protease derived from , in the presence of various organic solvents.
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