Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning

BACKGROUND

Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning, and design, as well as for understanding the functions of target. Although there are a few online platforms based on deep learning for drug-target interaction, affinity, and binding sites identification, there is currently no integrated online platforms for all three aspects.

RESULTS

Our solution, the novel integrated online platform Drug-Online, has been developed to facilitate drug screening, target identification, and understanding the functions of target in a progressive manner of "interaction-affinity-binding sites". Drug-Online platform consists of three parts: the first part uses the drug-target interaction identification method MGraphDTA, based on graph neural networks (GNN) and convolutional neural networks (CNN), to identify whether there is a drug-target interaction. If an interaction is identified, the second part employs the drug-target affinity identification method MMDTA, also based on GNN and CNN, to calculate the strength of drug-target interaction, i.e., affinity. Finally, the third part identifies drug-target binding sites, i.e., pockets. The method pt-lm-gnn used in this part is also based on GNN.

CONCLUSIONS

Drug-Online is a reliable online platform that integrates drug-target interaction, affinity, and binding sites identification. It is freely available via the Internet at http://39.106.7.26:8000/Drug-Online/ .

The freestanding sensor-based 3ω technique for measuring thermal conductivity of solids: principle and examination

In recent two decades, the 3ω technique has been proven to be valuable for characterizing thermophysical properties of materials from nanoscale to bulk, but some inherent deficiencies in this technique such as laborious and repeated four-pad micro strip heater/sensor deposition process and flimsiness of the micro heater/sensor limit its practical applications. Here, the authors report a novel 3ω technique, based on a freestanding sensor replacing the conventional 3ω heater/sensor adjacent to the specimen surface. A zigzag temperature response curve of the new sensor instead of the classical straight line was observed and used to extract the specimen thermal conductivity. Experimental results which excellently agree with calculation values show that the new technique is of great application value to thermal properties characterization of amorphous bulks and hundreds of microns thick wafers.

[Effects of vocalization and respiration and fiber connections on hyperstriatum ventrale pars caudale in Fringilla montifringilla]

In urethane-anesthetized Fringilla montifringilla, effects of electrically stimulating the hyperstriatum ventrale pars caudale (HVc) on vocalization and respiration were observed. Central connections of HVc were investigated by means of injecting CB-HRP into HVc. The results were as follows: (1) Electrical stimulation of HVc caused vocal response. (2) Long train electrical pulses stimulation of HVc elicited significant respiratory facilitating effects, that is, increase of respiratory rate and depth. (3) Short train stimulation administered in HVc during inspiratory phase terminated switching-off of inspiration, and during expiratory phases produced the prolongation of expiratory phase so to coordinate vocalization and then increasing the respiratory rate and depth. (4) CB-HRP traces revealed that HVc projected to robust nucleus of the archistriatum, and atea X of lobus parolfactorius. HVc received projections from medial nucleus magnocellularis of the anterior neostriatum, nucleus interfacialis of midneostriatum, telencephalic auditory nucleus-field L, nucleus uvaeformis of the thalamus, and locus ceruleus of the pons. These results showed that, besides vocal control, HVc may be involved in neural regulations of respiratory facilitation, the effect on respiration seeming specific. It is suggested that HVc may play an important role in coordinating singing and respiration.