Dataset Information

In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences.

ABSTRACT: Identification and validation of bioactive small-molecule targets is a significant challenge in drug discovery. In recent years, various in-silico approaches have been proposed to expedite time- and resource-consuming experiments for target detection. Herein, we developed several chemogenomic models for target prediction based on multi-scale information of chemical structures and protein sequences. By combining the information of a compound with multiple protein targets together and putting these compound-target pairs into a well-established model, the scores to indicate whether there are interactions between compounds and targets can be derived, and thus a target prediction task can be completed by sorting the outputted scores. To improve the prediction performance, we constructed several chemogenomic models using multi-scale information of chemical structures and protein sequences, and the ensemble model with the best performance was used as our final model. The model was validated by various strategies and external datasets and the promising target prediction capability of the model, i.e., the fraction of known targets identified in the top-k (1 to 10) list of the potential target candidates suggested by the model, was confirmed. Compared with multiple state-of-art target prediction methods, our model showed equivalent or better predictive ability in terms of the top-k predictions. It is expected that our method can be utilized as a powerful computational tool to narrow down the potential targets for experimental testing.

SUBMITTER: Yang SQ

PROVIDER: S-EPMC10123967 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences.

Yang Su-Qing SQ Zhang Liu-Xia LX Ge You-Jin YJ Zhang Jin-Wei JW Hu Jian-Xin JX Shen Cheng-Ying CY Lu Ai-Ping AP Hou Ting-Jun TJ Cao Dong-Sheng DS

Journal of cheminformatics 20230423 1

Identification and validation of bioactive small-molecule targets is a significant challenge in drug discovery. In recent years, various in-silico approaches have been proposed to expedite time- and resource-consuming experiments for target detection. Herein, we developed several chemogenomic models for target prediction based on multi-scale information of chemical structures and protein sequences. By combining the information of a compound with multiple protein targets together and putting thes ...[more]

PMID: 37088813

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Project description:In this study we introduce a hybrid ensemble consisting of air quality models operating at both the global and regional scale. The work is motivated by the fact that these different types of models treat specific portions of the atmospheric spectrum with different levels of detail, and it is hypothesized that their combination can generate an ensemble that performs better than mono-scale ensembles. A detailed analysis of the hybrid ensemble is carried out in the attempt to investigate this hypothesis and determine the real benefit it produces compared to ensembles constructed from only global-scale or only regional-scale models. The study utilizes 13 regional and 7 global models participating in the Hemispheric Transport of Air Pollutants phase 2 (HTAP2)-Air Quality Model Evaluation International Initiative phase 3 (AQMEII3) activity and focuses on surface ozone concentrations over Europe for the year 2010. Observations from 405 monitoring rural stations are used for the evaluation of the ensemble performance. The analysis first compares the modelled and measured power spectra of all models and then assesses the properties of the mono-scale ensembles, particularly their level of redundancy, in order to inform the process of constructing the hybrid ensemble. This study has been conducted in the attempt to identify that the improvements obtained by the hybrid ensemble relative to the mono-scale ensembles can be attributed to its hybrid nature. The improvements are visible in a slight increase of the diversity (4 % for the hourly time series, 10 % for the daily maximum time series) and a smaller improvement of the accuracy compared to diversity. Root mean square error (RMSE) improved by 13-16 % compared to G and by 2-3 % compared to R. Probability of detection (POD) and false-alarm rate (FAR) show a remarkable improvement, with a steep increase in the largest POD values and smallest values of FAR across the concentration ranges. The results show that the optimal set is constructed from an equal number of global and regional models at only 15 % of the stations. This implies that for the majority of the cases the regional-scale set of models governs the ensemble. However given the high degree of redundancy that characterizes the regional-scale models, no further improvement could be expected in the ensemble performance by adding yet more regional models to it. Therefore the improvement obtained with the hybrid set can confidently be attributed to the different nature of the global models. The study strongly reaffirms the importance of an in-depth inspection of any ensemble of opportunity in order to extract the maximum amount of information and to have full control over the data used in the construction of the ensemble.

Dataset Information

In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences.

Publications

In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences.

Similar Datasets

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