Your browser doesn't support javascript.
Adapt-Kcr: a novel deep learning framework for accurate prediction of lysine crotonylation sites based on learning embedding features and attention architecture.
Li, Zutan; Fang, Jingya; Wang, Shining; Zhang, Liangyun; Chen, Yuanyuan; Pian, Cong.
  • Li Z; College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
  • Fang J; College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
  • Wang S; Department of Mathematics, College of Science, Nanjing Agricultural University, China.
  • Zhang L; Department of Mathematics, College of Science, Nanjing Agricultural University, China.
  • Chen Y; Department of Mathematics, College of Science, Nanjing Agricultural University, China.
  • Pian C; Department of Mathematics, College of Science, Nanjing Agricultural University, China.
Brief Bioinform ; 23(2)2022 03 10.
Article in English | MEDLINE | ID: covidwho-1704326
ABSTRACT
Protein lysine crotonylation (Kcr) is an important type of posttranslational modification that is associated with a wide range of biological processes. The identification of Kcr sites is critical to better understanding their functional mechanisms. However, the existing experimental techniques for detecting Kcr sites are cost-ineffective, to a great need for new computational methods to address this problem. We here describe Adapt-Kcr, an advanced deep learning model that utilizes adaptive embedding and is based on a convolutional neural network together with a bidirectional long short-term memory network and attention architecture. On the independent testing set, Adapt-Kcr outperformed the current state-of-the-art Kcr prediction model, with an improvement of 3.2% in accuracy and 1.9% in the area under the receiver operating characteristic curve. Compared to other Kcr models, Adapt-Kcr additionally had a more robust ability to distinguish between crotonylation and other lysine modifications. Another model (Adapt-ST) was trained to predict phosphorylation sites in SARS-CoV-2, and outperformed the equivalent state-of-the-art phosphorylation site prediction model. These results indicate that self-adaptive embedding features perform better than handcrafted features in capturing discriminative information; when used in attention architecture, this could be an effective way of identifying protein Kcr sites. Together, our Adapt framework (including learning embedding features and attention architecture) has a strong potential for prediction of other protein posttranslational modification sites.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Protein Processing, Post-Translational / Computational Biology / Deep Learning / Lysine Type of study: Prognostic study Language: English Journal subject: Biology / Medical Informatics Year: 2022 Document Type: Article Affiliation country: Bib

Similar

MEDLINE

...
LILACS

LIS


Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Protein Processing, Post-Translational / Computational Biology / Deep Learning / Lysine Type of study: Prognostic study Language: English Journal subject: Biology / Medical Informatics Year: 2022 Document Type: Article Affiliation country: Bib