Harnessing Shape Complementarity for Upgraded Cyclohexane Purification through Adaptive Bottlenecked Pores in an Imidazole‐Containing MOF

Author(s):  
Chun-Rong Ye ◽  
Wen-Jian Wang ◽  
Wei Chen ◽  
Yonghong Xiao ◽  
Hai-Feng Zhang ◽  
...  
2020 ◽  
Vol 142 (27) ◽  
pp. 11680-11684
Author(s):  
Na Li ◽  
Fan Wu ◽  
Zihong Han ◽  
Xiaofeng Wang ◽  
Yi Liu ◽  
...  

2019 ◽  
Author(s):  
Georgy Derevyanko ◽  
Guillaume Lamoureux

AbstractProtein-protein interactions are determined by a number of hard-to-capture features related to shape complementarity, electrostatics, and hydrophobicity. These features may be intrinsic to the protein or induced by the presence of a partner. A conventional approach to protein-protein docking consists in engineering a small number of spatial features for each protein, and in minimizing the sum of their correlations with respect to the spatial arrangement of the two proteins. To generalize this approach, we introduce a deep neural network architecture that transforms the raw atomic densities of each protein into complex three-dimensional representations. Each point in the volume containing the protein is described by 48 learned features, which are correlated and combined with the features of a second protein to produce a score dependent on the relative position and orientation of the two proteins. The architecture is based on multiple layers of SE(3)-equivariant convolutional neural networks, which provide built-in rotational and translational invariance of the score with respect to the structure of the complex. The model is trained end-to-end on a set of decoy conformations generated from 851 nonredundant protein-protein complexes and is tested on data from the Protein-Protein Docking Benchmark Version 4.0.


Author(s):  
Raquel Norel ◽  
Donald Petrey ◽  
Haim J. Wolfson ◽  
Ruth Nussinov

Author(s):  
Chung-Jung Tsai ◽  
Raquel Norel ◽  
Haim J Wolfson ◽  
Jacob V Maizel ◽  
Ruth Nussinov

Molecules ◽  
2019 ◽  
Vol 24 (20) ◽  
pp. 3795 ◽  
Author(s):  
Laura Guedes ◽  
Pedro B. P. S. Reis ◽  
Miguel Machuqueiro ◽  
Asma Ressaissi ◽  
Rita Pacheco ◽  
...  

Centaurium erythraea is recommended for the treatment of gastrointestinal disorders and to reduce hypercholesterolemia in ethno-medicinal practice. To perform a top-down study that could give some insight into the molecular basis of these bioactivities, decoctions from C. erythraea leaves were prepared and the compounds were identified by liquid chromatography-high resolution tandem mass spectrometry (LC–MS/MS). Secoiridoids glycosides, like gentiopicroside and sweroside, and several xanthones, such as di-hydroxy-dimethoxyxanthone, were identified. Following some of the bioactivities previously ascribed to C. erythraea, we have studied its antioxidant capacity and the ability to inhibit acetylcholinesterase (AChE) and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR). Significant antioxidant activities were observed, following three assays: free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) reduction; lipoperoxidation; and NO radical scavenging capacity. The AChE and HMGR inhibitory activities for the decoction were also measured (56% at 500 μg/mL and 48% at 10 μg/mL, respectively). Molecular docking studies indicated that xanthones are better AChE inhibitors than gentiopicroside, while this compound exhibits a better shape complementarity with the HMGR active site than xanthones. To the extent of our knowledge, this is the first report on AChE and HMGR activities by C. erythraea decoctions, in a top-down analysis, complemented with in silico molecular docking, which aims to understand, at the molecular level, some of the biological effects ascribed to infusions from this plant.


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