Deep-AntiFP: Prediction of antifungal peptides using distanct multi-informative features incorporating with deep neural networks

被引:82
作者
Ahmad, Ashfaq [1 ]
Akbar, Shahid [1 ]
Khan, Salman [1 ]
Hayat, Maqsood [1 ]
Ali, Farman [2 ]
Ahmed, Aftab [1 ]
Tahir, Muhammad [1 ]
机构
[1] Abdul Wali Khan Univ, Dept Comp Sci, Mardan 23200, KP, Pakistan
[2] Nanjing Univ Sci & Technol, Sch Comp Sci & Engn, Nanjing 210094, Peoples R China
关键词
Antifungal peptides; Deep neural network; Multi-information fusion; Composite; Physiochemical properties; Support vector machine; Probabilistic neural network; MEMBRANE-PROTEIN TYPES; AMINO-ACID ALPHABET; RECOMBINATION SPOTS; ANTICANCER PEPTIDES; CLASSIFICATION; SYSTEM;
D O I
10.1016/j.chemolab.2020.104214
中图分类号
TP [自动化技术、计算机技术];
学科分类号
0812 ;
摘要
World widely, Fungal infections have become a serious issue for human beings. Fungal infections normally happen once invading fungus appear on a specific area of the body and become difficult for the human immune system to control. Current antifungal based therapies and drugs are deemed unsatisfactory due to their harmful side effects. Due to the rapid increase of this toxic disease in the human body, accurate identification of AFPs has become a challenging task for the researchers. Measuring the effectiveness of AFPs on the human body, a reliable intelligent model is highly indispensable for the accurate identification of Antifungal Peptides. In this study, high discriminative numerical descriptors are extracted from peptide sequences using composite physiochemical properties, quasi sequence order, and reduce amino acid alphabet. Furthermore, a multi-information fusion approach is also utilized for compensating the weakness of individual feature spaces. Finally, several classification learning methods are applied to choose a suitable operational engine for our model. After evaluating the empirical results, deep neural networks with hyper-parameter optimal values achieved an accuracy of 94.23%, 91.02%, and 89.08% using the training, alternate and independent dataset, respectively. It was found that our proposed "DeepAntiFP" outperformed and reported the highest performance than the existing computational models. It is expected that the developed model may be played a useful role in research academia as well as proteomics and drug development. The source code and all datasets are publicly available at https://github.com/shahidawkum/Deep-AntiFP.
引用
收藏
页数:10
相关论文
共 93 条
  • [31] Fang C., 2019, IPSJ Transact Bioinform, V12, P21, DOI DOI 10.2197/IPSJTBIO.12.21
  • [32] Learning Hierarchical Features for Scene Labeling
    Farabet, Clement
    Couprie, Camille
    Najman, Laurent
    LeCun, Yann
    [J]. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2013, 35 (08) : 1915 - 1929
  • [33] iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition
    Feng, Peng-Mian
    Chen, Wei
    Lin, Hao
    Chou, Kuo-Chen
    [J]. ANALYTICAL BIOCHEMISTRY, 2013, 442 (01) : 118 - 125
  • [34] Using deep neural network with small dataset to predict material defects
    Feng, Shuo
    Zhou, Huiyu
    Dong, Hongbiao
    [J]. MATERIALS & DESIGN, 2019, 162 : 300 - 310
  • [35] Fisher M.C., 2016, Tackling emerging fungal threats to animal health, food security and ecosystem resilience
  • [36] Emerging fungal threats to animal, plant and ecosystem health
    Fisher, Matthew C.
    Henk, Daniel. A.
    Briggs, Cheryl J.
    Brownstein, John S.
    Madoff, Lawrence C.
    McCraw, Sarah L.
    Gurr, Sarah J.
    [J]. NATURE, 2012, 484 (7393) : 186 - 194
  • [37] WRF-TMH: predicting transmembrane helix by fusing composition index and physicochemical properties of amino acids
    Hayat, Maqsood
    Khan, Asifullah
    [J]. AMINO ACIDS, 2013, 44 (05) : 1317 - 1328
  • [38] Mem-PHybrid: Hybrid features-based prediction system for classifying membrane protein types
    Hayat, Maqsood
    Khan, Asifullah
    [J]. ANALYTICAL BIOCHEMISTRY, 2012, 424 (01) : 35 - 44
  • [39] Deep Neural Networks for Acoustic Modeling in Speech Recognition
    Hinton, Geoffrey
    Deng, Li
    Yu, Dong
    Dahl, George E.
    Mohamed, Abdel-rahman
    Jaitly, Navdeep
    Senior, Andrew
    Vanhoucke, Vincent
    Patrick Nguyen
    Sainath, Tara N.
    Kingsbury, Brian
    [J]. IEEE SIGNAL PROCESSING MAGAZINE, 2012, 29 (06) : 82 - 97
  • [40] BS-KNN: An Effective Algorithm for Predicting Protein Subchloroplast Localization
    Hu, Jing
    Yan, Xianghe
    [J]. EVOLUTIONARY BIOINFORMATICS, 2012, 8 : 79 - 87