iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor
Defensins as 1 of major classes of host defense peptides play a significant role in the innate immunity, which are extremely evolved in almost all living organisms. Developing high-throughput computational methods can accurately help in designing drugs or medical means to defense against pathogens....
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2019-07-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.1177/1176934319867088 |
| _version_ | 1818304939320934400 |
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| author | Yongchun Zuo Yu Chang Shenghui Huang Lei Zheng Lei Yang Guifang Cao |
| author_facet | Yongchun Zuo Yu Chang Shenghui Huang Lei Zheng Lei Yang Guifang Cao |
| author_sort | Yongchun Zuo |
| collection | DOAJ |
| description | Defensins as 1 of major classes of host defense peptides play a significant role in the innate immunity, which are extremely evolved in almost all living organisms. Developing high-throughput computational methods can accurately help in designing drugs or medical means to defense against pathogens. To take up such a challenge, an up-to-date server based on rigorous benchmark dataset, referred to as iDEF-PseRAAC, was designed for predicting the defensin family in this study. By extracting primary sequence compositions based on different types of reduced amino acid alphabet, it was calculated that the best overall accuracy of the selected feature subset was achieved to 92.38%. Therefore, we can conclude that the information provided by abundant types of amino acid reduction will provide efficient and rational methodology for defensin identification. And, a free online server is freely available for academic users at http://bioinfor.imu.edu.cn/idpf . We hold expectations that iDEF-PseRAAC may be a promising weapon for the function annotation about the defensins protein. |
| first_indexed | 2024-12-13T06:18:40Z |
| format | Article |
| id | doaj.art-ab012f3e59ed489f81abb881b18995c2 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-13T06:18:40Z |
| publishDate | 2019-07-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-ab012f3e59ed489f81abb881b18995c22022-12-21T23:56:55ZengSAGE PublishingEvolutionary Bioinformatics1176-93432019-07-011510.1177/1176934319867088iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition DescriptorYongchun Zuo0Yu Chang1Shenghui Huang2Lei Zheng3Lei Yang4Guifang Cao5State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, ChinaState Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, ChinaState Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, ChinaState Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, ChinaCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, ChinaCollege of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, ChinaDefensins as 1 of major classes of host defense peptides play a significant role in the innate immunity, which are extremely evolved in almost all living organisms. Developing high-throughput computational methods can accurately help in designing drugs or medical means to defense against pathogens. To take up such a challenge, an up-to-date server based on rigorous benchmark dataset, referred to as iDEF-PseRAAC, was designed for predicting the defensin family in this study. By extracting primary sequence compositions based on different types of reduced amino acid alphabet, it was calculated that the best overall accuracy of the selected feature subset was achieved to 92.38%. Therefore, we can conclude that the information provided by abundant types of amino acid reduction will provide efficient and rational methodology for defensin identification. And, a free online server is freely available for academic users at http://bioinfor.imu.edu.cn/idpf . We hold expectations that iDEF-PseRAAC may be a promising weapon for the function annotation about the defensins protein.https://doi.org/10.1177/1176934319867088 |
| spellingShingle | Yongchun Zuo Yu Chang Shenghui Huang Lei Zheng Lei Yang Guifang Cao iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor Evolutionary Bioinformatics |
| title | iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor |
| title_full | iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor |
| title_fullStr | iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor |
| title_full_unstemmed | iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor |
| title_short | iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor |
| title_sort | idef pseraac identifying the defensin peptide by using reduced amino acid composition descriptor |
| url | https://doi.org/10.1177/1176934319867088 |
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