Dataset Information

DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates.

ABSTRACT: The enzyme turnover rate, ${k}_{cat}$, quantifies enzyme kinetics by indicating the maximum efficiency of enzyme catalysis. Despite its importance, ${k}_{cat}$ values remain scarce in databases for most organisms, primarily because of the cost of experimental measurements. To predict ${k}_{cat}$ and account for its strong temperature dependence, DLTKcat was developed in this study and demonstrated superior performance (log10-scale root mean squared error = 0.88, R-squared = 0.66) than previously published models. Through two case studies, DLTKcat showed its ability to predict the effects of protein sequence mutations and temperature changes on ${k}_{cat}$ values. Although its quantitative accuracy is not high enough yet to model the responses of cellular metabolism to temperature changes, DLTKcat has the potential to eventually become a computational tool to describe the temperature dependence of biological systems.

SUBMITTER: Qiu S

PROVIDER: S-EPMC10772988 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Publications

DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates.

Qiu Sizhe S Zhao Simiao S Yang Aidong A

Briefings in bioinformatics 20231101 1

The enzyme turnover rate, ${k}_{cat}$, quantifies enzyme kinetics by indicating the maximum efficiency of enzyme catalysis. Despite its importance, ${k}_{cat}$ values remain scarce in databases for most organisms, primarily because of the cost of experimental measurements. To predict ${k}_{cat}$ and account for its strong temperature dependence, DLTKcat was developed in this study and demonstrated superior performance (log10-scale root mean squared error = 0.88, R-squared = 0.66) than previously ...[more]

PMID: 38189538

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Project description:Background Substation equipment temperature is difficult to achieve accurate prediction because of its typical seasonality, periodicity and instability, complex working environment and less available characteristic information. Methods To overcome these difficulties, a substation equipment temperature prediction method is proposed based on multivariate information fusion, convolutional neural network (CNN) and gated recurrent unite (GRU) in this article. Firstly, according to the correlation analysis including linear correlation mapping, autocorrelation function and partial autocorrelation function for substation equipment temperature data, the feature vectors from ambient, time and space are determined, that is the multivariate information fusion feature vector (denoted as MIFFV); secondly, the dimension of MIFFV is reduced by principal component analysis (PCA), extract some of the most important features and form the reduced feature vector (denoted as RFV); then, CNN is used for deep learning to extract the relationship between RFV and the high-dimensional space feature, and construct the high-dimensional feature vector of multivariate time series (denoted as HDFV); finally, the high-dimensional feature vector is used to train GRU deep learning network and predict the equipment temperature. Results A substation equipment in Taizhou City, Zhejiang Province is conducted by the method proposed in this article. Through the comparative experiment from the two aspects of features and methods, under the two prediction performance evaluation indexes of mean absolute percentage error (MAPE) and root mean square error (RSME), two main conclusions are drawn: (1) MIFFV from three aspects of ambient features, time features and space features have better prediction performance than the single feature vector and the combined feature vector of two aspects; (2) compared with other four related models under the same conditions, RFV is regarded as the input of the models, the proposed model has better prediction performance.

Dataset Information

DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates.

Publications

DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates.

Similar Datasets

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