Bioactive Peptide Screening and Evaluation

The biological activity of the peptides was evaluated using the online tool PeptideRanker (http://distilldeep.ucd.ie/PeptideRanker/). PeptideRanker is a platform based on an advanced neural network model specifically designed to predict the potential bioactivity of the peptides (Coscueta, Batista, Gomes, da Silva, & Pintado, 2022 (link)). The model assigns a probability value to peptides within an activity prediction range of 0–1. Peptides with a score above 0.8 were identified as potential bioactive candidates for further screening. ToxinPred (https://crdd.osdd.net/raghava/toxinpred/) and AllerTOP (https://www.ddg-pharmfac.net/allertop/index.html) were also used to predict toxicity and evaluate the allergenicity of the peptides, respectively.

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Dang K., Lan J., Wang Y., Pan D., Du L., Suo S., Dang Y, & Gao X. (2025). Screening and evaluation of novel DPP-IV inhibitory peptides in goat milk based on molecular docking and molecular dynamics simulation. Food Chemistry: X, 25, 102217.

Publication 2025

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Variable analysis

independent variables

The independent variables are not explicitly mentioned in the provided information.

dependent variables

The dependent variable is the biological activity of the peptides, which was evaluated using the PeptideRanker tool.

control variables

The control variables are not explicitly mentioned in the provided information.

controls

The authors used two additional tools, ToxinPred and AllerTOP, to predict the toxicity and evaluate the allergenicity of the peptides, respectively. These can be considered as positive and negative controls for the peptide screening process.

Annotations

Based on most similar protocols

Optimize the PeptideRanker tool by using a threshold of 0.5 or 0.8 to identify potential bioactive peptides (Protocol 2, Protocol 4, Protocol 5).

Use ToxinPred to predict the toxicity of the peptides and exclude potentially toxic ones (Protocol 2, Protocol 3, Protocol 5).

Employ AllerTOP to evaluate the allergenicity of the peptides, especially those with high hydrophobicity (80% hydrophobic amino acids) (Protocol 5).

Determine the chemical properties, such as hydrophobicity, charge, isoelectric point, and amphipathicity, using online tools like Innovagen and PEPTIDE 2.0 (Protocol 3, Protocol 5).

Consider using additional in silico tools to predict other potential bioactivities, such as antioxidant and ACE inhibitory properties, using AnOxPePred-1.0 and mAHTPred (Protocol 3).

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