Models and data of AMPlify: a deep learning tool for antimicrobial peptide prediction. 2023

Chenkai Li, and René L Warren, and Inanc Birol
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.

OBJECTIVE Antibiotic resistance is a rising global threat to human health and is prompting researchers to seek effective alternatives to conventional antibiotics, which include antimicrobial peptides (AMPs). Recently, we have reported AMPlify, an attentive deep learning model for predicting AMPs in databases of peptide sequences. In our tests, AMPlify outperformed the state-of-the-art. We have illustrated its use on data describing the American bullfrog (Rana [Lithobates] catesbeiana) genome. Here we present the model files and training/test data sets we used in that study. The original model (the balanced model) was trained on a balanced set of AMP and non-AMP sequences curated from public databases. In this data note, we additionally provide a model trained on an imbalanced set, in which non-AMP sequences far outnumber AMP sequences. We note that the balanced and imbalanced models would serve different use cases, and both would serve the research community, facilitating the discovery and development of novel AMPs. METHODS This data note provides two sets of models, as well as two AMP and four non-AMP sequence sets for training and testing the balanced and imbalanced models. Each model set includes five single sub-models that form an ensemble model. The first model set corresponds to the original model trained on a balanced training set that has been described in the original AMPlify manuscript, while the second model set was trained on an imbalanced training set.

UI MeSH Term Description Entries
D011892 Rana catesbeiana A species of the family Ranidae (true frogs). The only anuran properly referred to by the common name "bullfrog", it is the largest native anuran in North America. Bullfrog,Bullfrogs,Rana catesbeianas,catesbeiana, Rana
D000077321 Deep Learning Supervised or unsupervised machine learning methods that use multiple layers of data representations generated by nonlinear transformations, instead of individual task-specific ALGORITHMS, to build and train neural network models. Hierarchical Learning,Learning, Deep,Learning, Hierarchical
D000089882 Antimicrobial Peptides Small peptides that play an important role in early innate and induced defenses against invading microbes. Most have positive overall charges and are referred to as cationic antimicrobial peptides. Antimicrobial Peptide,Peptide, Antimicrobial
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D000900 Anti-Bacterial Agents Substances that inhibit the growth or reproduction of BACTERIA. Anti-Bacterial Agent,Anti-Bacterial Compound,Anti-Mycobacterial Agent,Antibacterial Agent,Antibiotics,Antimycobacterial Agent,Bacteriocidal Agent,Bacteriocide,Anti-Bacterial Compounds,Anti-Mycobacterial Agents,Antibacterial Agents,Antibiotic,Antimycobacterial Agents,Bacteriocidal Agents,Bacteriocides,Agent, Anti-Bacterial,Agent, Anti-Mycobacterial,Agent, Antibacterial,Agent, Antimycobacterial,Agent, Bacteriocidal,Agents, Anti-Bacterial,Agents, Anti-Mycobacterial,Agents, Antibacterial,Agents, Antimycobacterial,Agents, Bacteriocidal,Anti Bacterial Agent,Anti Bacterial Agents,Anti Bacterial Compound,Anti Bacterial Compounds,Anti Mycobacterial Agent,Anti Mycobacterial Agents,Compound, Anti-Bacterial,Compounds, Anti-Bacterial

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