Literature DB >> 35693256

Research on DNA-Binding Protein Identification Method Based on LSTM-CNN Feature Fusion.

Weizhong Lu1,2, Xiaoyi Chen1, Yu Zhang3, Hongjie Wu1, Yijie Ding4, Jiawei Shen1, Shixuan Guan1, Haiou Li1.   

Abstract

Protein is closely related to life activities. As a kind of protein, DNA-binding protein plays an irreplaceable role in life activities. Therefore, it is very important to study DNA-binding protein, which is a subject worthy of study. Although traditional biotechnology has high precision, its cost and efficiency are increasingly unable to meet the needs of modern society. Machine learning methods can make up for the deficiencies of biological experimental techniques to a certain extent, but they are not as simple and fast as deep learning for data processing. In this paper, a deep learning framework based on parallel long and short-term memory(LSTM) and convolutional neural networks(CNN) was proposed to identify DNA-binding protein. This model can not only further extract the information and features of protein sequences, but also the features of evolutionary information. Finally, the two features are combined for training and testing. On the PDB2272 dataset, compared with PDBP_Fusion model, Accuracy(ACC) and Matthew's Correlation Coefficient (MCC) increased by 3.82% and 7.98% respectively. The experimental results of this model have certain advantages.
Copyright © 2022 Weizhong Lu et al.

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Year:  2022        PMID: 35693256      PMCID: PMC9184165          DOI: 10.1155/2022/9705275

Source DB:  PubMed          Journal:  Comput Math Methods Med        ISSN: 1748-670X            Impact factor:   2.809


  23 in total

Review 1.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Authors:  A A Schäffer; L Aravind; T L Madden; S Shavirin; J L Spouge; Y I Wolf; E V Koonin; S F Altschul
Journal:  Nucleic Acids Res       Date:  2001-07-15       Impact factor: 16.971

2.  Enabling full-length evolutionary profiles based deep convolutional neural network for predicting DNA-binding proteins from sequence.

Authors:  Sucheta Chauhan; Shandar Ahmad
Journal:  Proteins       Date:  2019-07-08

3.  PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou's PseAAC and Physicochemical Distance Transformation.

Authors:  Bin Liu; Jinghao Xu; Shixi Fan; Ruifeng Xu; Jiyun Zhou; Xiaolong Wang
Journal:  Mol Inform       Date:  2014-09-26       Impact factor: 3.353

4.  An Improved Protein Structural Classes Prediction Method by Incorporating Both Sequence and Structure Information.

Authors: 
Journal:  IEEE Trans Nanobioscience       Date:  2014-09-15       Impact factor: 2.935

5.  DPP-PseAAC: A DNA-binding protein prediction model using Chou's general PseAAC.

Authors:  M Saifur Rahman; Swakkhar Shatabda; Sanjay Saha; M Kaykobad; M Sohel Rahman
Journal:  J Theor Biol       Date:  2018-05-16       Impact factor: 2.691

6.  Prediction of DNA binding proteins using local features and long-term dependencies with primary sequences based on deep learning.

Authors:  Guobin Li; Xiuquan Du; Xinlu Li; Le Zou; Guanhong Zhang; Zhize Wu
Journal:  PeerJ       Date:  2021-05-03       Impact factor: 2.984

7.  DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation.

Authors:  Bin Liu; Shanyi Wang; Xiaolong Wang
Journal:  Sci Rep       Date:  2015-10-20       Impact factor: 4.379

8.  On the prediction of DNA-binding proteins only from primary sequences: A deep learning approach.

Authors:  Yu-Hui Qu; Hua Yu; Xiu-Jun Gong; Jia-Hui Xu; Hong-Shun Lee
Journal:  PLoS One       Date:  2017-12-29       Impact factor: 3.240

9.  DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.

Authors:  Mu Gao; Jeffrey Skolnick
Journal:  Nucleic Acids Res       Date:  2008-05-31       Impact factor: 16.971

10.  A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks.

Authors:  Peng Zhang; Lin Tao; Xian Zeng; Chu Qin; Shangying Chen; Feng Zhu; Zerong Li; Yuyang Jiang; Weiping Chen; Yu-Zong Chen
Journal:  Brief Bioinform       Date:  2017-11-01       Impact factor: 11.622

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