Transferable high dimensional neural network potentials (HDNNPs) have shown great promise as an avenue to increase the accuracy and domain of applicability of existing atomistic force fields for organic systems relevant to life science. We have previously reported such a potential (Schrödinger-ANI) that has broad coverage of druglike molecules. We extend that work here to cover ionic and zwitterionic druglike molecules expected to be relevant to drug discovery research activities. We report a novel HDNNP architecture, which we call QRNN, that predicts atomic charges and uses these charges as descriptors in an energy model that delivers conformational energies within chemical accuracy when measured against the reference theory it is trained to. Further, we find that delta learning based on a semiempirical level of theory approximately halves the errors. We test the models on torsion energy profiles, relative conformational energies, geometric parameters, and relative tautomer errors.
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J Autism Dev Disord
December 2024
School of Information Science and Engineering, Yanshan University, Qinhuangdao, 066004, China.
Autism spectrum disorder (ASD) has been reported to exhibit altered local functional consistency. However, previous studies mainly focused on male samples and explored the temporal consistency in the ASD brain ignoring the spatial consistency. In this study, FOur-dimensional Consistency of local neural Activities (FOCA) analysis was used to investigate the sex differences of local spatiotemporal consistency of spontaneous brain activity in ASD.
View Article and Find Full Text PDFACS Appl Mater Interfaces
December 2024
TCS Research, Sahyadri Park 2, Rajiv Gandhi Infotech Park, Hinjewadi Phase 3, Pune 411057, India.
Realization of a sustainable hydrogen economy in the future requires the development of efficient and cost-effective catalysts for its production at scale. MXenes (MX) are a class of 2D materials with 'n' layers of carbon or nitrogen (X) interleaved by 'n+1' layers of transition metal (M) and have emerged as promising materials for various applications including catalysts for hydrogen evolution reaction (HER). Their properties are intimately related to both their composition and their atomic structure.
View Article and Find Full Text PDFBMC Cancer
December 2024
Department of Data Science, Faculty of Interdisciplinary Science and Technology, Tarbiat Modares University, Tehran, Iran.
Glioblastoma Multiforme (GBM), classified as a grade IV glioma by the World Health Organization (WHO), is a prevalent and notably aggressive form of brain tumor derived from glial cells. It stands as one of the most severe forms of primary brain cancer in humans. The median survival time of GBM patients is only 12-15 months, making it the most lethal type of brain tumor.
View Article and Find Full Text PDFBMC Bioinformatics
December 2024
School of Computer Engineering, Jiangsu Ocean University, Lianyungang, 222005, China.
Background: Cancer classification has consistently been a challenging problem, with the main difficulties being high-dimensional data and the collection of patient samples. Concretely, obtaining patient samples is a costly and resource-intensive process, and imbalances often exist between samples. Moreover, expression data is characterized by high dimensionality, small samples and high noise, which could easily lead to struggles such as dimensionality catastrophe and overfitting.
View Article and Find Full Text PDFBMC Genomics
December 2024
School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China.
Background: The subcellular localization of mRNA plays a crucial role in gene expression regulation and various cellular processes. However, existing wet lab techniques like RNA-FISH are usually time-consuming, labor-intensive, and limited to specific tissue types. Researchers have developed several computational methods to predict mRNA subcellular localization to address this.
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