In structure-based drug design, scoring functions are often employed to evaluate protein–ligand interactions. A variety of scoring functions have been developed so far, and thus, some objective ...benchmarks are desired for assessing their strength and weakness. The comparative assessment of scoring functions (CASF) benchmark developed by us provides an answer to this demand. CASF is designed as a “scoring benchmark”, where the scoring process is decoupled from the docking process to depict the performance of scoring function more precisely. Here, we describe the latest update of this benchmark, i.e., CASF-2016. Each scoring function is still evaluated by four metrics, including “scoring power”, “ranking power”, “docking power”, and “screening power”. Nevertheless, the evaluation methods have been improved considerably in several aspects. A new test set is compiled, which consists of 285 protein–ligand complexes with high-quality crystal structures and reliable binding constants. A panel of 25 scoring functions are tested on CASF-2016 as a demonstration. Our results reveal that the performance of current scoring functions is more promising in terms of docking power than scoring, ranking, and screening power. Scoring power is somewhat correlated with ranking power, so are docking power and screening power. The results obtained on CASF-2016 may provide valuable guidance for the end users to make smart choices among available scoring functions. Moreover, CASF is created as an open-access benchmark so that other researchers can utilize it to test a wider range of scoring functions. The complete CASF-2016 benchmark will be released on the PDBbind-CN web server (http://www.pdbbind-cn.org/casf.asp/) once this article is published.
Recently, Hyperspectral Image (HSI) classification has gradually been getting attention from more and more researchers. HSI has abundant spectral and spatial information; thus, how to fuse these two ...types of information is still a problem worth studying. In this paper, to extract spectral and spatial feature, we propose a Double-Branch Multi-Attention mechanism network (DBMA) for HSI classification. This network has two branches to extract spectral and spatial feature respectively which can reduce the interference between the two types of feature. Furthermore, with respect to the different characteristics of these two branches, two types of attention mechanism are applied in the two branches respectively, which ensures to extract more discriminative spectral and spatial feature. The extracted features are then fused for classification. A lot of experiment results on three hyperspectral datasets shows that the proposed method performs better than the state-of-the-art method.
In structure-based drug design, scoring functions are widely used for fast evaluation of protein–ligand interactions. They are often applied in combination with molecular docking and de novo design ...methods. Since the early 1990s, a whole spectrum of protein–ligand interaction scoring functions have been developed. Regardless of their technical difference, scoring functions all need data sets combining protein–ligand complex structures and binding affinity data for parametrization and validation. However, data sets of this kind used to be rather limited in terms of size and quality. On the other hand, standard metrics for evaluating scoring function used to be ambiguous. Scoring functions are often tested in molecular docking or even virtual screening trials, which do not directly reflect the genuine quality of scoring functions. Collectively, these underlying obstacles have impeded the invention of more advanced scoring functions. In this Account, we describe our long-lasting efforts to overcome these obstacles, which involve two related projects. On the first project, we have created the PDBbind database. It is the first database that systematically annotates the protein–ligand complexes in the Protein Data Bank (PDB) with experimental binding data. This database has been updated annually since its first public release in 2004. The latest release (version 2016) provides binding data for 16 179 biomolecular complexes in PDB. Data sets provided by PDBbind have been applied to many computational and statistical studies on protein–ligand interaction and various subjects. In particular, it has become a major data resource for scoring function development. On the second project, we have established the Comparative Assessment of Scoring Functions (CASF) benchmark for scoring function evaluation. Our key idea is to decouple the “scoring” process from the “sampling” process, so scoring functions can be tested in a relatively pure context to reflect their quality. In our latest work on this track, i.e. CASF-2013, the performance of a scoring function was quantified in four aspects, including “scoring power”, “ranking power”, “docking power”, and “screening power”. All four performance tests were conducted on a test set containing 195 high-quality protein–ligand complexes selected from PDBbind. A panel of 20 standard scoring functions were tested as demonstration. Importantly, CASF is designed to be an open-access benchmark, with which scoring functions developed by different researchers can be compared on the same grounds. Indeed, it has become a popular choice for scoring function validation in recent years. Despite the considerable progress that has been made so far, the performance of today’s scoring functions still does not meet people’s expectations in many aspects. There is a constant demand for more advanced scoring functions. Our efforts have helped to overcome some obstacles underlying scoring function development so that the researchers in this field can move forward faster. We will continue to improve the PDBbind database and the CASF benchmark in the future to keep them as useful community resources.
Na+ plays a vital role in numerous physiological processes across humans and animals, necessitating a comprehensive understanding of Na+ transmembrane transport. Among the various Na+ pumps and ...channels, light-driven Na+-pumping rhodopsin (NaR) has emerged as a noteworthy model in this field. This review offers a concise overview of the structural and functional studies conducted on NaR, encompassing ground/intermediate-state structures and photocycle kinetics. The primary focus lies in addressing key inquiries: (1) unraveling the translocation pathway of Na+; (2) examining the role of structural changes within the photocycle, particularly in the O state, in facilitating Na+ transport; and (3) investigating the timing of Na+ uptake/release. By delving into these unresolved issues and existing debates, this review aims to shed light on the future direction of Na+ pump research.
With the rapid development of Internet movie industry social-aware movie recommendation systems (SMRs) have become a popular online web service that provide relevant movie recommendations to users. ...In this effort many existing movie recommendation approaches learn a user ranking model from user feedback with respect to the movie's content. Unfortunately this approach suffers from the sparsity problem inherent in SMR data. In the present work we address the sparsity problem by learning a multimodal network representation for ranking movie recommendations. We develop a heterogeneous SMR network for movie recommendation that exploits the textual description and movie-poster image of each movie as well as user ratings and social relationships. With this multimodal data we then present a heterogeneous information network learning framework called SMR-multimodal network representation learning (MNRL) for movie recommendation. To learn a ranking metric from the heterogeneous information network we also developed a multimodal neural network model. We evaluated this model on a large-scale dataset from a real world SMR Web site and we find that SMR-MNRL achieves better performance than other state-of-the-art solutions to the problem.
The uniformity of the excitation magnetic field is an important factor affecting the measurement accuracy of the electromagnetic flowmeter and its adaptability to different flow states of the complex ...multiphase flow. The main purpose of this paper is to improve the measurement accuracy of electromagnetic flowmeter by improving the uniformity of magnetic field excitation of electromagnetic flowmeter sensor. Firstly, an evaluation index system based on area weight magnetic field deviation degree is established, and the concept of flow state adaptability is put forward. According to this evaluation system, the excitation structure of the conventional electromagnetic flowmeter sensor is improved and optimized, and an excitation model with high uniformity is designed. Meanwhile, the ANSYS software is used for numerical simulation, and normalized standard deviation is used to compare between the new and the traditional electromagnetic flowmeter models. Finally, according to the requirements of the index function, the magnetic pole detection angle of the improved excitation model is simulated and analyzed, and the optimal magnetic pole detection angle is determined to be 45°. On this basis, a new electromagnetic flowmeter is designed for complex multiphase flow at oil wellhead. The field test proves that the measurement error of this flowmeter can reach less than 5%. Compared with the traditional electromagnetic flowmeter, the measurement accuracy has been greatly improved.
A diagnosis scheme using the Hurst exponent for metal particle faults in GIL/GIS is proposed to improve the accuracy of classification and identification. First, the diagnosis source signal is the ...vibration signal generated by the collision of metal particles in the electric field. Then, the signal is processed via variational mode decomposition (VMD) based on particle swarm optimization with adaptive parameter adjustment (APA-PSO). In the end, fault types are classified and identified by an SVM model, whose feature vector is composed of the Hurst exponents of each intrinsic mode function (IMF-H). Extensive experimental data verify the effect of this new scheme. The results exhibit that the classification performance of SVM is significantly improved by the new feature vector. Furthermore, the VMD based on APA-PSO with adaptive parameter adjustment can effectively enhance the decomposition quality.
With the development of smart warehouses in Industry 4.0, scheduling a fleet of automated guided vehicles (AGVs) for transporting and sorting parcels has become a new development trend. In smart ...warehouses, AGVs receive paths from the multi-AGV scheduling system and independently sense the surrounding environment while sending poses as interactive information. This navigation method relies heavily on on-board sensors and significantly increases the information interactions within the system. Under this situation, a solution that locates multiple AGVs in global images of the warehouse by top cameras is expected to have a great effect. However, traditional tracking algorithms cannot output the heading angles required by the AGV navigation and their real-time performance and calculation accuracy cannot satisfy the tracking of large-scale AGVs. Therefore, this paper proposes a multi-AGV tracking system that integrates a multi-AGV scheduling system, AprilTag system, improved YOLOv5 with the oriented bounding box (OBB), extended Kalman filtering (EKF), and global vision to calculate the coordinates and heading angles of AGVs. Extensive experiments prove that in addition to less time complexity, the multi-AGV tracking system can efficiently track a fleet of AGVs with higher positioning accuracy than traditional navigation methods and other tracking algorithms based on various location patterns.
Abstract
Background
This study performed a randomized trial data meta-analysis to assess The Modified Brostrom-Gould (MBG) for proven chronic lateral ankle instability (CLAI).
Methods
All published ...randomized clinical trials comparing MBG and other operations were found by searching the Cochrane Library, EMBASE, and PubMed databases. The Review Manager 5.4 software was used to compare the two groups regarding postoperative functional score, ankle stability, and complications. Risk Ratio (RR) and Mean Differences (MD) were used in meta-analyses.
Results
8 experiments are suitable for it, 426 patients were enrolled, and 222 patients underwent other operations surgery. Among the six outcome indicators, in terms of FAOS scores, the other operations group has an advantage, 6.53 points higher than MBG; others show no significant differences.
Conclusions
Based on this meta-analysis, the authors believe that other surgical groups can achieve better outcomes than MBG in some aspects of CLAI treatment.
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