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A long path has led from the determination of the first protein structure in 1960 to the recent breakthroughs in protein science. Protein structure prediction and design methodologies based on machine learning (ML) have been recognized with the 2024 Nobel prize in Chemistry, but they would not have been possible without previous work and the input of many domain scientists. Challenges remain in the application of ML tools for the prediction of structural ensembles and their usage within the software pipelines for structure determination by crystallography or cryogenic electron microscopy. In the drug discovery workflow, ML techniques are being used in diverse areas such as scoring of docked poses, or the generation of molecular descriptors. As the ML techniques become more widespread, novel applications emerge which can profit from the large amounts of data available. Nevertheless, it is essential to balance the potential advantages against the environmental costs of ML deployment to decide if and when it is best to apply it. For hit to lead optimization ML tools can efficiently interpolate between compounds in large chemical series but free energy calculations by molecular dynamics simulations seem to be superior for designing novel derivatives. Importantly, the potential complementarity and/or synergism of physics-based methods (, force field-based simulation models) and data-hungry ML techniques is growing strongly. Current ML methods have evolved from decades of research. It is now necessary for biologists, physicists, and computer scientists to fully understand advantages and limitations of ML techniques to ensure that the complementarity of physics-based methods and ML tools can be fully exploited for drug design.
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http://dx.doi.org/10.1039/d4md00869c | DOI Listing |
BMJ Open Ophthalmol
March 2025
Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Caserta, Italy.
Aim: To evaluate the efficacy and safety of direct selective laser trabeculoplasty (DSLT) on eyes with primary open-angle glaucoma (POAG) and on primary angle closure glaucoma (PACG) eyes at 1 year follow-up.
Methods: In this study, 54 patients affected by POAG (76) or PACG (28) undergoing DSLT were enrolled, for a total of 104 eyes. Before each treatment and at each follow-up visit, all subjects underwent a complete eye visit, including the collection of data regarding the number and type of topical medications prescribed for glaucoma.
Free Radic Biol Med
March 2025
Institute of Structural Pharmacology & TCM Chemical Biology, Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; Wuya College of Innovation, School of Pharmacy, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China. Electronic address:
Ischemic stroke represents a predominant cause of morbidity and mortality globally, resulting from abrupt vascular occlusion or rupture, which precipitates considerable neuronal damage. This study aims to shed more light on the specific neuroprotective mechanisms of Kirenol, a bioactive diterpene derived from traditional herbal medicine, with a particular focus on its regulation of mitochondrial dynamics via the CK2/AKT signalling pathway and its impact on the mitochondrial fusion protein Optic atrophy 1 (Opa1). The effects of Kirenol on neuronal viability, mitochondrial function, and pertinent signalling pathways were evaluated by employing a middle cerebral artery occlusion (MCAO) model in rats and subjecting HT22 neuronal cells to oxidative stress.
View Article and Find Full Text PDFAntiviral Res
March 2025
Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China, 8 Huaying Road, Baiyun District, Guangzhou, Guangdong Province, 510663, China; Scientific Research Center, Shanghai Public Health Clinical Center, Shanghai, 201508, China. Electronic address:
The covalently closed circular DNA (cccDNA) of the Hepatitis B virus (HBV) serves as a template for producing progeny viruses in virally infected hepatocytes. Promising cccDNA-targeting antiviral agents remain unavailable and unpredictable in the research and development pipelines, making sterile HBV elimination challenging at the current stage. The major challenge of discriminating trace amounts of cccDNA from the abundant HBV relaxed circular DNA (rcDNA), which is nearly identical to cccDNA in sequence, substantially discourages efforts to discover and directly screen cccDNA-targeting drugs.
View Article and Find Full Text PDFJ Pharm Sci
March 2025
State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, 999078, China; Faculty of Health Sciences, University of Macau, Macau, 999078, China. Electronic address:
Cyclodextrin formulations are crucial for enhancing the solubility of drugs. Bile salts are recognized as potential agents for displacing drugs from cyclodextrin formulations in intestinal fluids. However, the mechanism underlying this displacement remains unclear.
View Article and Find Full Text PDFJ Struct Biol
March 2025
Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India. Electronic address:
Dengue pathogen, transmitted by mosquitoes, poses a growing threat as it is capable of inflicting severe illness in humans. Around 40% of the global population is currently affected by the virus, resulting in thousands of fatalities each year. The genetic blueprint of the virus comprises 10 proteins.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!