Apoferritin tilt series and frame series used to benchmark the resolution of both data types in M
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ABSTRACT:
SUBMITTER: Dimitry Tegunov
PROVIDER: EMPIAR-10491 | biostudies-other |
REPOSITORIES: biostudies-other
Similar Datasets
Project description: Not available
| EMPIAR-11543 | biostudies-other
Project description:Identifying membrane proteins and their multi-functional types is an indispensable yet challenging topic in proteomics and bioinformatics. In this article, we provide data that are used for training and testing Mem-ADSVM (Wan et al., 2016. "Mem-ADSVM: a two-layer multi-label predictor for identifying multi-functional types of membrane proteins" [1]), a two-layer multi-label predictor for predicting multi-functional types of membrane proteins.
| S-EPMC4889873 | biostudies-other
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| EMPIAR-11257 | biostudies-other
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| EMPIAR-10377 | biostudies-other
Project description:In the automotive industry, machinery failures of the resistance spot welding (RSW) guns would interrupt the manufacturing lines and cause unplanned downtime, potentially resulting in a significant loss of production and reliability. Predicting the machinery failures of the RSW gun can provide more scientific strategies for predictive maintenance and decision-making. However, fault prediction of RSW guns has become increasingly challenging due to their complex behavior and data variability. In this paper, we created a benchmark dataset and proposed welding gun fault prediction benchmarks to aid in the development of machine learning approaches toward welding gun fault prediction. The dataset was collected at the Body-Shop (BS) of BMW Brilliance Automotive Ltd. from different components of hundreds of RSW guns to capture the patterns and trends before welding errors with historical data. Then we provide state-of-the-art machine learning (ML) benchmarks on time series forecasting methods in a welding gun fault prediction use case. This study will provide insights for time series forecasting while enabling ML researchers to contribute towards the fault prediction of the RSW guns.
| S-EPMC10796372 | biostudies-literature
Project description:BackgroundHelical membrane proteins are vital for the interaction of cells with their environment. Predicting the location of membrane helices in protein amino acid sequences provides substantial understanding of their structure and function and identifies membrane proteins in sequenced genomes. Currently there is no comprehensive benchmark tool for evaluating prediction methods, and there is no publication comparing all available prediction tools. Current benchmark literature is outdated, as recently determined membrane protein structures are not included. Current literature is also limited to global assessments, as specialised benchmarks for predicting specific classes of membrane proteins were not previously carried out.DescriptionWe present a benchmark server at http://sydney.edu.au/pharmacy/sbio/software/TMH_benchmark.shtml that uses recent high resolution protein structural data to provide a comprehensive assessment of the accuracy of existing membrane helix prediction methods. The server further allows a user to compare uploaded predictions generated by novel methods, permitting the comparison of these novel methods against all existing methods compared by the server. Benchmark metrics include sensitivity and specificity of predictions for membrane helix location and orientation, and many others. The server allows for customised evaluations such as assessing prediction method performances for specific helical membrane protein subtypes.We report results for custom benchmarks which illustrate how the server may be used for specialised benchmarks. Which prediction method is the best performing method depends on which measure is being benchmarked. The OCTOPUS membrane helix prediction method is consistently one of the highest performing methods across all measures in the benchmarks that we performed.ConclusionsThe benchmark server allows general and specialised assessment of existing and novel membrane helix prediction methods. Users can employ this benchmark server to determine the most suitable method for the type of prediction the user needs to perform, be it general whole-genome annotation or the prediction of specific types of helical membrane protein. Creators of novel prediction methods can use this benchmark server to evaluate the performance of their new methods. The benchmark server will be a valuable tool for researchers seeking to extract more sophisticated information from the large and growing protein sequence databases.
| S-EPMC3620685 | biostudies-literature
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| EMPIAR-10378 | biostudies-other
Project description: Not available
| EMPIAR-11273 | biostudies-other
Project description:Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than ?4?nm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology.
| S-EPMC6389375 | biostudies-literature
Project description:We used a differential Pavlovian conditioning paradigm to measure tilt aftereffect (TAE) strength. Gabor patches, rotated clockwise and anticlockwise, were used as conditioned stimuli (CSs), one of which (CS+) was followed by the unconditioned stimulus (UCS), whereas the other (CS-) appeared alone. The UCS was an air puff delivered to the left eye. In addition to the CS+ and CS-, the vertical test patch was also presented for the clockwise and anticlockwise adapters. The vertical patch was not followed by the UCS. After participants acquired differential conditioning, eyeblink conditioned responses (CRs) were observed for the vertical patch when it appeared to be tilted in the same direction as the CS+ owing to the TAE. The effect was observed not only when the adapter and test stimuli were presented in the same retinotopic position but also when they were presented in the same spatiotopic position, although spatiotopic TAE was weak-it occurred approximately half as often as the full effect. Furthermore, spatiotopic TAE decayed as the time after saccades increased, but did not decay as the time before saccades increased. These results suggest that the time before the performance of saccadic eye movements is needed to compute the spatiotopic representation.
| S-EPMC5240094 | biostudies-literature