Prediction of antioxidant peptides using a quantitative structure-activity relationship predictor (AnOxPP) based on bidirectional long short-term memory neural network and interpretable amino acid descriptors. 2023

Dongya Qin, and Linna Jiao, and Ruihong Wang, and Yi Zhao, and Youjin Hao, and Guizhao Liang
Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400030, China.

Antioxidant peptides can protect against free radical-mediated diseases, especially food-derived antioxidant peptides are considered as potential competitors among synthetic antioxidants due to their safety, high activity and abundant sources. However, wet experimental methods can not meet the need for effectively screening and clearly elucidating the structure-activity relationship of antioxidant peptides. Therefore, it is particularly important to build a reliable prediction platform for antioxidant peptides. In this work, we developed a platform, AnOxPP, for prediction of antioxidant peptides using the bidirectional long short-term memory (BiLSTM) neural network. The sequence characteristics of peptides were converted into feature codes based on amino acid descriptors (AADs). Our results showed that the feature conversion ability of the combined-AADs optimized by the forward feature selection method was more accurate than that of the single-AADs. Especially, the model trained by the optimal descriptor SDPZ27 significantly outperformed the existing predictor on two independent test sets (Accuracy = 0.967 and 0.819, respectively). The SDPZ27-based AnOxPP learned four key structure-activity features of antioxidant peptides, with the following importance as steric properties > hydrophobic properties > electronic properties > hydrogen bond contributions. AnOxPP is a valuable tool for screening and design of peptide drugs, and the web-server is accessible at http://www.cqudfbp.net/AnOxPP/index.jsp.

UI MeSH Term Description Entries
D008570 Memory, Short-Term Remembrance of information for a few seconds to hours. Immediate Recall,Memory, Immediate,Working Memory,Memory, Shortterm,Immediate Memories,Immediate Memory,Immediate Recalls,Memories, Immediate,Memories, Short-Term,Memories, Shortterm,Memory, Short Term,Recall, Immediate,Recalls, Immediate,Short-Term Memories,Short-Term Memory,Shortterm Memories,Shortterm Memory,Working Memories
D010455 Peptides Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are considered to be larger versions of peptides that can form into complex structures such as ENZYMES and RECEPTORS. Peptide,Polypeptide,Polypeptides
D000596 Amino Acids Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins. Amino Acid,Acid, Amino,Acids, Amino
D000975 Antioxidants Naturally occurring or synthetic substances that inhibit or retard oxidation reactions. They counteract the damaging effects of oxidation in animal tissues. Anti-Oxidant,Antioxidant,Antioxidant Activity,Endogenous Antioxidant,Endogenous Antioxidants,Anti-Oxidant Effect,Anti-Oxidant Effects,Anti-Oxidants,Antioxidant Effect,Antioxidant Effects,Activity, Antioxidant,Anti Oxidant,Anti Oxidant Effect,Anti Oxidant Effects,Anti Oxidants,Antioxidant, Endogenous,Antioxidants, Endogenous
D016571 Neural Networks, Computer A computer architecture, implementable in either hardware or software, modeled after biological neural networks. Like the biological system in which the processing capability is a result of the interconnection strengths between arrays of nonlinear processing nodes, computerized neural networks, often called perceptrons or multilayer connectionist models, consist of neuron-like units. A homogeneous group of units makes up a layer. These networks are good at pattern recognition. They are adaptive, performing tasks by example, and thus are better for decision-making than are linear learning machines or cluster analysis. They do not require explicit programming. Computational Neural Networks,Connectionist Models,Models, Neural Network,Neural Network Models,Neural Networks (Computer),Perceptrons,Computational Neural Network,Computer Neural Network,Computer Neural Networks,Connectionist Model,Model, Connectionist,Model, Neural Network,Models, Connectionist,Network Model, Neural,Network Models, Neural,Network, Computational Neural,Network, Computer Neural,Network, Neural (Computer),Networks, Computational Neural,Networks, Computer Neural,Networks, Neural (Computer),Neural Network (Computer),Neural Network Model,Neural Network, Computational,Neural Network, Computer,Neural Networks, Computational,Perceptron
D021281 Quantitative Structure-Activity Relationship A quantitative prediction of the biological, ecotoxicological or pharmaceutical activity of a molecule. It is based upon structure and activity information gathered from a series of similar compounds. Structure Activity Relationship, Quantitative,3D-QSAR,QSAR,QSPR Modeling,Quantitative Structure Property Relationship,3D QSAR,3D-QSARs,Modeling, QSPR,Quantitative Structure Activity Relationship,Quantitative Structure-Activity Relationships,Relationship, Quantitative Structure-Activity,Relationships, Quantitative Structure-Activity,Structure-Activity Relationship, Quantitative,Structure-Activity Relationships, Quantitative

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