Allosteric regulation, the most direct and efficient way of regulating protein function, is induced by the binding of a ligand at one site that is topographically distinct from an orthosteric site. Allosteric Database (ASD, available online at http://mdl.shsmu.edu.cn/ASD) has been developed to provide comprehensive information featuring allosteric regulation. With increasing data, fundamental questions pertaining to allostery are currently receiving more attention from the mechanism of allosteric changes in an individual protein to the entire effect of the changes in the interconnected network in the cell. Thus, the following novel features were added to this updated version: (i) structural mechanisms of more than 1600 allosteric actions were elucidated by a comparison of site structures before and after the binding of an modulator; (ii) 261 allosteric networks were identified to unveil how the allosteric action in a single protein would propagate to affect downstream proteins; (iii) two of the largest human allosteromes, protein kinases and GPCRs, were thoroughly constructed; and (iv) web interface and data organization were completely redesigned for efficient access. In addition, allosteric data have largely expanded in this update. These updates are useful for facilitating the investigation of allosteric mechanisms, dynamic networks and drug discoveries.
This paper advocates a novel video saliency detection method based on the spatial-temporal saliency fusion and low-rank coherency guided saliency diffusion. In sharp contrast to the conventional methods, which conduct saliency detection locally in a frame-by-frame way and could easily give rise to incorrect low-level saliency map, in order to overcome the existing difficulties, this paper proposes to fuse the color saliency based on global motion clues in a batch-wise fashion. And we also propose low-rank coherency guided spatial-temporal saliency diffusion to guarantee the temporal smoothness of saliency maps. Meanwhile, a series of saliency boosting strategies are designed to further improve the saliency accuracy. First, the original long-term video sequence is equally segmented into many short-term frame batches, and the motion clues of the individual video batch are integrated and diffused temporally to facilitate the computation of color saliency. Then, based on the obtained saliency clues, inter-batch saliency priors are modeled to guide the low-level saliency fusion. After that, both the raw color information and the fused low-level saliency are regarded as the low-rank coherency clues, which are employed to guide the spatial-temporal saliency diffusion with the help of an additional permutation matrix serving as the alternative rank selection strategy. Thus, it could guarantee the robustness of the saliency map's temporal consistence, and further boost the accuracy of the computed saliency map. Moreover, we conduct extensive experiments on five public available benchmarks, and make comprehensive, quantitative evaluations between our method and 16 state-of-the-art techniques. All the results demonstrate the superiority of our method in accuracy, reliability, robustness, and versatility.
Matrix inversion often arises in the fields of science and engineering. Many models for matrix inversion usually assume that the solving process is free of noises or that the denoising has been conducted before the computation. However, time is precious for the real-time-varying matrix inversion in practice, and any preprocessing for noise reduction may consume extra time, possibly violating the requirement of real-time computation. Therefore, a new model for time-varying matrix inversion that is able to handle simultaneously the noises is urgently needed. In this paper, an integration-enhanced Zhang neural network (IEZNN) model is first proposed and investigated for real-time-varying matrix inversion. Then, the conventional ZNN model and the gradient neural network model are presented and employed for comparison. In addition, theoretical analyses show that the proposed IEZNN model has the global exponential convergence property. Moreover, in the presence of various kinds of noises, the proposed IEZNN model is proven to have an improved performance. That is, the proposed IEZNN model converges to the theoretical solution of the time-varying matrix inversion problem no matter how large the matrix-form constant noise is, and the residual errors of the proposed IEZNN model can be arbitrarily small for time-varying noises and random noises. Finally, three illustrative simulation examples, including an application to the inverse kinematic motion planning of a robot manipulator, are provided and analyzed to substantiate the efficacy and superiority of the proposed IEZNN model for real-time-varying matrix inversion.
Based on a bio-heuristic algorithm, this paper proposes a novel path planner called obstacle avoidance beetle antennae search (OABAS) algorithm, which is applied to the global path planning of unmanned aerial vehicles (UAVs). Compared with the previous bio-heuristic algorithms, the algorithm proposed in this paper has advantages of a wide search range and breakneck search speed, which resolves the contradictory requirements of the high computational complexity of the bio-heuristic algorithm and real-time path planning of UAVs. Besides, the constraints used by the proposed algorithm satisfy various characteristics of the path, such as shorter path length, maximum allowed turning angle, and obstacle avoidance. Ignoring the z-axis optimization by combining with the minimum threat surface (MTS), the resultant path meets the requirements of efficiency and safety. The effectiveness of the algorithm is substantiated by applying the proposed path planning algorithm on the UAVs. Moreover, comparisons with other existing algorithms further demonstrate the superiority of the proposed OABAS algorithm.
Adenosine-5’-triphosphate (ATP) is generally regarded as a substrate for energy currency and protein modification. Recent findings uncovered the allosteric function of ATP in cellular signal transduction but little is understood about this critical behavior of ATP. Through extensive analysis of ATP in solution and proteins, we found that the free ATP can exist in the compact and extended conformations in solution, and the two different conformational characteristics may be responsible for ATP to exert distinct biological functions: ATP molecules adopt both compact and extended conformations in the allosteric binding sites but conserve extended conformations in the substrate binding sites. Nudged elastic band simulations unveiled the distinct dynamic processes of ATP binding to the corresponding allosteric and substrate binding sites of uridine monophosphate kinase, and suggested that in solution ATP preferentially binds to the substrate binding sites of proteins. When the ATP molecules occupy the allosteric binding sites, the allosteric trigger from ATP to fuel allosteric communication between allosteric and functional sites is stemmed mainly from the triphosphate part of ATP, with a small number from the adenine part of ATP. Taken together, our results provide overall understanding of ATP allosteric functions responsible for regulation in biological systems.
The quality of inverse problem solutions obtained through deep learning [Barbastathis et al, 2019] is limited by the nature of the priors learned from examples presented during the training phase. In the case of quantitative phase retrieval [Sinha et al 2017, Goy et al 2019], in particular, spatial frequencies that are underrepresented in the training database, most often at the high band, tend to be suppressed in the reconstruction. Ad hoc solutions have been proposed, such as pre-amplifying the high spatial frequencies in the examples [Li et al, 2018]; however, while that strategy improves resolution, it also leads to high-frequency artifacts as well as lowfrequency distortions in the reconstructions. Here, we present a new approach that learns separately how to handle the two frequency bands, low and high; and also learns how to synthesize these two bands into the full-band reconstructions. We show that this "learning to synthesize" (LS) method yields phase reconstructions of high spatial resolution and artifact-free; and it is also resilient to high-noise conditions, e.g. in the case of very low photon flux. In addition to the problem of quantitative phase retrieval, the LS method is applicable, in principle, to any inverse problem where the forward operator treats different frequency bands unevenly, i.e. is ill-posed.
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