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Until recently, computational tools were mainly used to explain chemical reactions after experimental results were obtained. With the rapid development of software and hardware technologies to make computational modeling tools more reliable, they can now provide valuable insights and even become predictive. In this review, we highlighted several studies involving computational predictions of unexpected reactivities or providing mechanistic insights for organic and organometallic reactions that led to improved experimental results. Key to these successful applications is an integration between theory and experiment that allows for incorporation of empirical knowledge with precise computed values. Computer modeling of chemical reactions is already a standard tool that is being embraced by an ever increasing group of researchers, and it is clear that its utility in predictive reaction design will increase further in the near future.
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http://dx.doi.org/10.1021/acs.chemrev.9b00073 | DOI Listing |
Oncogene
September 2025
Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
Cholesterol biosynthesis is more activated in triple negative breast cancer (TNBC) than in other subtype breast cancer and plays essential role in facilitating TNBC. However, the regulatory network and how cholesterol biosynthesis contribute to TNBC development and progression are not well elucidated. Here, we found that reticulum membrane protein complex 2 (EMC2) is highly expressed in TNBC and predicts short survival of patients.
View Article and Find Full Text PDFJ Chem Inf Model
September 2025
School of Medicine and Warshel Institute for Computational Biology, The Chinese University of Hong Kong─Shenzhen, Shenzhen, Guangdong 518172, China.
Argonaute (Ago) is a DNA-guided programmable endonuclease with emerging applications in genome engineering, yet the rate-determining dynamic mechanisms governing its transition from guide-target hybridization to catalytic activation remain unresolved. Here, we employ molecular dynamics simulations and the Traveling-salesman-based Automated Path Searching (TAPS) approach to dissect the target DNA recognition in the middle region (nt 9-12) of Ago. We designed two paths to tackle this problem: one assumed that coordination of the target DNA backbone occurs before base-pairing between the target and guide DNA; the other hypothesized a concerted transition without preferred order between backbone-coordination and base-pairing.
View Article and Find Full Text PDFJ Neurosci
September 2025
Psychiatry, University of Minnesota, Minneapolis, Minnesota 55455
Deep brain stimulation (DBS) is an emerging treatment for otherwise treatment-refractory psychiatric disorders. It can produce remarkable clinical results in expert hands, but has not fared as well in controlled, multisite trials. That difficulty with scaling up arises in part because DBS' mechanisms are poorly understood, meaning that it is difficult to objectively identify patients likely to respond and/or to customize stimulation to match individual patients' needs.
View Article and Find Full Text PDFHeart
September 2025
Department of Biomedical Engineering, CARIM Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
Cardiovascular disease remains a leading cause of morbidity and mortality worldwide, with conventional management often applying standardised approaches that struggle to address individual variability in increasingly complex patient populations. Computational models, both knowledge-driven and data-driven, have the potential to reshape cardiovascular medicine by offering innovative tools that integrate patient-specific information with physiological understanding or statistical inference to generate insights beyond conventional diagnostics. This review traces how computational modelling has evolved from theoretical research tools into clinical decision support systems that enable personalised cardiovascular care.
View Article and Find Full Text PDFNucleic Acids Res
September 2025
Department of Microbiology, Institute of Biology, University of Kassel, 34132 Kassel, Germany.
Casein kinase 1 (CK1) family members are crucial for ER-Golgi trafficking, calcium signalling, DNA repair, transfer RNA (tRNA) modifications, and circadian rhythmicity. Whether and how substrate interactions and kinase autophosphorylation contribute to CK1 plasticity remains largely unknown. Here, we undertake a comprehensive phylogenetic, cellular, and molecular characterization of budding yeast CK1 Hrr25 and identify human CK1 epsilon (CK1ϵ) as its ortholog.
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