Methodology and Score
The tool identifies potential AMP domains within longer amino acid chains. The algorithm moves a "sliding window" along the sequence (step 1 aa e.g. 1-12, 2-13, 3-14 etc.), evaluating key parameters for membrane interaction. Each point on the chart represents the Score for the entire fragment starting at a given position.
Bacterial membranes are negatively charged. The algorithm sums charges in the window (K/R=+1, D/E=-1, H=+0.5). If the net charge is ≥ +2, the score is multiplied (bonus x1.5), promoting strong attraction to bacteria. Negative charges are penalized (-3 pts).
AMP peptides must penetrate the lipid membrane. Optimal hydrophobicity (-0.5 to +1.5) is rewarded (x2). Values outside this range (too polar or too hydrophobic) receive penalty points (-1 or -2).
The α-helix structure is crucial. Proline (P) acts as a "helix breaker", whereas Glycine (G) is generally tolerated; however, its accumulation (e.g., three residues in close proximity) destabilizes the helix, resulting in a penalty score (-2).
AMP Domain Biophysical Profile
The chart presents the AMP domain potential for consecutive sliding windows in the sequence. A higher score (Score > 5.0) indicates a higher probability of antimicrobial activity.
Proposed Candidates (Top Hits)
| Rank | Position | Sequence (Window) | Charge | Hydro | Score | Action |
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