The development and benchmarking of computational chemistry methods rely on comparison with benchmark data. More and larger benchmark datasets are becoming available, and working efficiently with them is a necessity. The Cuby framework provides rich functionality for working with datasets, comes with many ready-to-use predefined benchmark sets, and interfaces with a wide range of computational chemistry software packages. Here, we review the tools Cuby provides for working with datasets and provide examples of more advanced workflows, such as handling large numbers of computations on high performance computing resources and reusing previously computed data. Cuby has also been extended recently to include two important benchmark databases, NCIAtlas and GMTKN55.
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http://dx.doi.org/10.1063/5.0203372 | DOI Listing |
Data Brief
February 2025
Mulago National Referral Hospital, P.O Box 7051, Kampala, Uganda.
Malaria is a major public health challenge in sub-Saharan Africa. Timely and accurate diagnosis of malaria is vital to reduce the caseload and mortality rates associated with malaria The use of microscopy in malaria screening is the gold standard recommended method by the World Health Organisation (WHO). In Uganda, utilization of microscopy is challenged by insufficient expertise to interpret the images accurately, affecting the efficiency, effectiveness and accuracy of malaria detection and diagnosis.
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December 2024
ByteDance Research Bellevue Washington 98004 USA
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges.
View Article and Find Full Text PDFMethodsX
June 2025
Assistant Professor, Department of Electronics and Communication Engineering, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Tamil Nadu, 600062, India.
Glaucoma, a severe eye disease leading to irreversible vision loss if untreated, remains a significant challenge in healthcare due to the complexity of its detection. Traditional methods rely on clinical examinations of fundus images, assessing features like optic cup and disc sizes, rim thickness, and other ocular deformities. Recent advancements in artificial intelligence have introduced new opportunities for enhancing glaucoma detection.
View Article and Find Full Text PDFCogn Neurodyn
December 2025
School of Computer Science, Hangzhou Dianzi University, Hangzhou, 310018 Zhejiang China.
Brainprint recognition technology, regarded as a promising biometric technology, encounters challenges stemming from the time-varied, low signal-to-noise ratio of brain signals, such as electroencephalogram (EEG). Steady-state visual evoked potentials (SSVEP) exhibit high signal-to-noise ratio and frequency locking, making them a promising paradigm for brainprint recognition. Consequently, the extraction of time-invariant identity information from SSVEP EEG signals is essential.
View Article and Find Full Text PDFSpatial transcriptomics data analysis integrates gene expression profiles with their corresponding spatial locations to identify spatial domains, infer cell-type dynamics, and detect gene expression patterns within tissues. However, the current spatial transcriptomics analysis neglects the multiscale cell-cell interactions that are crucial in biology. To fill this gap, we propose multiscale cell-cell interactive spatial transcriptomics (MCIST) analysis.
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