Modern drug discovery typically faces large virtual screens from huge compound databases where multiple docking tools are involved for meeting various real scenes or improving the precision of virtual screens. Among these tools, AutoDock Vina and its numerous derivatives are the most popular and have become the standard pipeline for molecular docking in modern drug discovery. Our recent Vina-GPU method realized 14-fold acceleration against AutoDock Vina on a piece of NVIDIA RTX 3090 GPU in one virtual screening case. Further speedup of AutoDock Vina and its derivatives with GPUs is beneficial to systematically push their popularization in large-scale virtual screens due to their high benefit-cost ratio and easy operation for users. Thus, we proposed the Vina-GPU 2.0 method to further accelerate AutoDock Vina and the most common derivatives with new docking algorithms (QuickVina 2 and QuickVina-W) with GPUs. Caused by the discrepancy of their docking algorithms, our Vina-GPU 2.0 adopts different GPU acceleration strategies. In virtual screening for two hot protein kinase targets RIPK1 and RIPK3 from the DrugBank database, our Vina-GPU 2.0 reaches an average of 65.6-fold,1.4-fold and 3.6-fold docking acceleration against the original AutoDock Vina, QuickVina 2 and QuickVina-W while ensuring their comparable docking accuracy. In addition, we develop a friendly and installation-free graphical user interface (GUI) tool for their convenient usage. The codes and tools of Vina-GPU 2.0 are freely available at https://github.com/DeltaGroupNJUPT/Vina-GPU-2.0, coupled with explicit instructions and examples.
Next-generation 6G networks will fully drive the development of the industrial Internet of Things. Steel surface defect detection as an important application in industrial Internet of Things has recently received increasing attention from the military industry, the aviation industry and other fields, which is closely related to the quality of industrial production products. However, many typical convolutional neural networks-based methods are insensitive to the problem of unclear boundaries. In this article, the authors develop a region-based fully convolutional networks with deformable convolution and attention fusion to adaptively learn salient features for steel surface defect detection. Specifically, deformable convolution is applied into selectively replace the standard convolution in the backbone of the region-based fully convolutional networks, which performs significantly in scenarios with unclear defect boundaries. Moreover, convolutional block attention module is utilised in region proposal network to further enhance detection accuracy. The proposed architecture is demonstrated on two popular steel defect detection benchmarks, including NEU-DET and GC10-DET, which can effectively present the performance of steel surface defect detection by abundant experiments. The mean average precision on two datasets reaches 80.9% and 66.2%. The average precision of defect crazing, inclusion, patches, pitted-surface, rolled-in scale and scratches on NEU-DET is 58.2%, 82.3%, 95.7%, 85.6%, 75.9%, and 87.9% respectively.
AutoDock VINA is one of the most-used docking tools in the early stage of modern drug discovery. It uses a Monte-Carlo based iterated search method and multithreading parallelism scheme on multicore machines to improve docking accuracy and speed. However, virtual screening from huge compound databases is common for modern drug discovery, which puts forward a great demand for higher docking speed of AutoDock VINA. Therefore, we propose a fast method VINA-GPU, which expands the Monte-Carlo based docking lanes into thousands of ones coupling with a largely reduced number of search steps in each lane. Furthermore, we develop a heterogeneous OpenCL implementation of VINA-GPU that leverages thousands of computational cores of a GPU, and obtains a maximum of 403-fold acceleration on docking runtime when compared with a quad-threaded AutoDock VINA implementation. In addition, a heuristic function was fitted to determine the proper size of search steps in each lane for a convenient usage. The VINA-GPU code can be freely available at https://github.com/DeltaGroupNJUPT/VINA-GPU for academic usage.
Diabetes is a common complication that happened in pregnant women, and it often leads to many serious consequences for fetuses and gravidas. Accurate diagnosis of gestational diabetes mellitus (GDM) is the key to providing prompt and precise treatment and disease management. The artificial intelligence-based method is currently the most commonly used auxiliary way for clinical medical diagnosis. However, as all we know, there is no report on the assistance of GDM diagnosis based on artificial intelligence till now. In this work, we collected the clinical samples of 1000 pregnant women from ZhongDa Hospital of Southeast University in Nanjing city, which involves 221 cases of GDM. Then, a matrix factorization method was used to fill up all missing values in the original data. Next, a random forest model was adopted to evaluate the importance of each feature dimension to aid in finding potential clinical markers for the GDM diagnosis. Finally, a novel transformer-based method called TF-GDM was proposed for predicting gestational diabetes mellitus accurately. The results show that our TF-GDM method achieves excellent performance, with the accuracy, precision, and recall of 0.93, 0.88, and 0.92, respectively, and also with the F1 score and AUC value of 0.90 and 0.94, respectively. The results demonstrate that our TF-GDM method is significantly better than classic machine learning-based and deep learning-based methods.
AutoDock VINA is one of the most-used docking tools in the early stage of modern drug discovery. It uses a Monte-Carlo based iterated search method and multithreading parallelism scheme on multicore machines to improve docking accuracy and speed. However, virtual screening from huge compound databases is common for modern drug discovery, which puts forward a great demand for higher docking speed of AutoDock VINA. Therefore, we propose a fast method VINA-GPU, which expands the Monte-Carlo based docking lanes into thousands of ones coupling with a largely reduced number of search steps in each lane. Furthermore, we develop a heterogeneous OpenCL implementation of VINA-GPU that leverages thousands of computational cores of a GPU, and obtains a maximum of 403-fold acceleration on docking runtime when compared with a quad-threaded AutoDock VINA implementation. In addition, a heuristic function was fitted to determine the proper size of search steps in each lane for a convenient usage. The VINA-GPU code can be freely available at https://github.com/DeltaGroupNJUPT/Vina-GPU for academic usage.
AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best docking power among all the docking tools. Modern drug discovery is facing the most common scenario on large virtual screening of drug hits from huge compound databases. Due to the seriality characteristic of the AutoDock Vina algorithm, there is no successful report on its parallel acceleration with GPUs. Current acceleration of AutoDock Vina typically relies on the stack of computing power as well as the allocation of resource and tasks, such as the VirtualFlow platform. The vast resource expenditure and the high access threshold of users will seriously limit the popularity of AutoDock Vina and the flexibility of usage in modern drug discovery. Thus, the design of a new method for accelerating AutoDock Vina with GPUs is greatly needed for reducing the investment for large virtual screens, and also for a wide application in large-scale virtual screening on personal computers, station servers orcloud computing etc. Our proposed method Vina-GPU greatly raises the number of initial random conformations and reduces the search depth of each lane, and then a heterogeneous OpenCL implementation was developed to realize its parallel acceleration leveraging thousands of GPU cores. Large benchmarks show that Vina-GPU reaches a maximum of 403- fold docking acceleration against the original AutoDock Vina while ensuring their comparable docking accuracy, indicating its potential of pushing the popularization of AutoDock Vina in large virtual screens. The Vina-GPU code and tool can be freely available at http:// www.noveldelta.com/Vina_GPU for academic usage.
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