Prediction of transport proteins from sequence information with the deep learning approach.
Comput Biol Med
; 160: 106974, 2023 06.
Article
em En
| MEDLINE
| ID: mdl-37167658
ABSTRACT
Transport proteins (TPs) are vital to the growth and life of all living things, especially in fields of microbial pathogenesis and drug resistance of tumor cells. Accurately identifying potential TPs remains an important challenge for the advancement of functional genomics. This study aimed to develop a tool for predicting TPs using the deep learning approach. Here, we proposed DeepTP, a convolutional neural network model that uses parallel subnetworks to extract features from protein sequences and uses fully connected layers for TP classification. To train and evaluate the performance of the developed model, datasets were collected from the UniProtKB/Swiss-Prot database. The test results revealed that the proposed model could successfully identify TPs with the AUCROC, accuracy, F-value, and Matthews correlation coefficient of 0.9719, 0.9513, 0.8982, and 0.8679, respectively. By further comparison, DeepTP achieved better performance than other commonly used methods. Analysis of the gradients of prediction score concerning input suggested that DeepTP makes predictions by recognizing the functional domains of TPs. We anticipate that DeepTP will serve as a useful tool for predicting TPs in large-scale genome projects, which will facilitate the discovery of novel TPs.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Aprendizado Profundo
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Comput Biol Med
Ano de publicação:
2023
Tipo de documento:
Article
País de afiliação:
China