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Artificial intelligence in peptide-based drug design.
Drug Discov Today
January 2025
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China. Electronic address:
Protein-protein interactions (PPIs) are fundamental to a variety of biological processes, but targeting them with small molecules is challenging because of their large and complex interaction interfaces. However, peptides have emerged as highly promising modulators of PPIs, because they can bind to protein surfaces with high affinity and specificity. Nonetheless, computational peptide design remains difficult, hindered by the intrinsic flexibility of peptides and the substantial computational resources required.
View Article and Find Full Text PDFA minimal model of cognition based on oscillatory and current-based reinforcement processes.
J R Soc Interface
January 2025
Department of Information Technology, Uppsala University, Uppsala, Sweden.
Building mathematical models of brains is difficult because of the sheer complexity of the problem. One potential starting point is basal cognition, which gives an abstract representation of a range of organisms without central nervous systems, including fungi, slime moulds and bacteria. We propose one such model, demonstrating how a combination of oscillatory and current-based reinforcement processes can be used to couple resources in an efficient manner, mimicking the way these organisms function.
View Article and Find Full Text PDFMaternal exposures are known to influence the risk of isolated cleft lip with or without cleft palate (CL/P) - a common and highly heritable birth defect with a multifactorial etiology. To identify new CL/P risk loci, we conducted a genome-wide gene-environment interaction (GEI) analysis of CL/P on a sample of 540 cases and 260 controls recruited from the Philippines, incorporating the interaction effects of genetic variants with maternal smoking and vitamin use. As GEI analyses are typically low in power and the results can be difficult to interpret, we used multiple testing frameworks to evaluate potential GEI effects: 1 degree-of-freedom (1df) GxE test, the 3df joint test, and the two-step EDGE approach.
View Article and Find Full Text PDFGenerative Model for Constructing Reaction Path from Initial to Final States.
J Chem Theory Comput
January 2025
Preferred Networks, Inc., Tokyo 100-0004, Japan.
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths can be difficult for humans. This paper presents an innovative approach that utilizes neural networks to generate initial guesses for reaction pathways based on the initial state and learning from a database of low-energy transition paths.
View Article and Find Full Text PDFCreating pragmatic, rapid-cycle, evidence-based innovation: The Kaiser Permanente Northern California Delivery Science and Applied Research (DARE) program.
Learn Health Syst
January 2025
Division of Research Kaiser Permanente Northern California Oakland California USA.
Introduction: Ongoing crises in the quality, affordability, sustainability, value, and equity of U.S. healthcare call for rapid, massive-scale innovations across multiple specialties.
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