Tools for Antimicrobial Peptides
There are additional tools for antimicrobial peptide research and some can be accessed below.
1. Predict antimicrobial peptides
You can try select prediction tools in the APD Links.
2. Predict the cleavage sites of signal peptides
You can use Signal4.1 to do so.
3. Identify antimicrobial peptides most similar to your new peptide
You can find out by using the APD prediction tool here. You need click on "do alignment" after "showing me the helix formation".
4. Peptide helical wheel
One of the links for doing this is here.
5. Hydrophobicity and Hydrophobic moment
You can figure it out here.
6. GRAVY and Wimley-White whole-residue hydrophobicity
The grand average hydropathy and the Wimley-White whole-residue hydrophobicity have been programmed into the APD and can be calculated using the APD calculatation tool by entering the peptide amino acid sequence.
7. Boman index (i.e. protein-binding potential)
Boman index (see Glossary for defintion) can be calculated using the APD tool here by entering the peptide amino acid sequence.
8. Peptide net charge, hydrophobic percentage and amino acid compostion
Peptide net charge, hydrophobic content, and amino acid compostion can be calculated using this APD tool.
9. Peptide molecular weight, molecular formula and extinction coefficient
Peptide molecular weight, molecular formula, and extinction coefficient for UV quantification can be calculated using the tool link.
10. Peptide isoelectric point pI, estimated half life, instability index and aliphatic index calculations
All these parameters can be calculated here ExPASy.
11. Peptide half life in intestine-like exvironment
It can be estimated using the HLP tool.
12. Peptide cell penetrating ability
This ability can be determined by CellPPD tool.
13. Peptide antigenicity, allergic potential and toxicity
This ability can be determined by antigenic prediction.
14. Multiple peptide sequence alignment
You can do the multiple sequence alignment of either polypeptides or nucleic acids using ClustalW2.
15. Peptide stability: predict the potential cleavage sites by proteases or chemicals
You can use Peptide Cutter.
16. Identify a possible precursor sequence of your peptide
You may find the precursor sequence of your AMP by using Peptide Match.
17. Full chain protein structure prediction for academic users
You may predict the structure of protein-like AMPs such as defensins using Rosetta. Another structure prediction program is I-TASSER.
18. HPLC retention time prediction
You can predict it using Retention Prediction Server.
19. Translate tool
You can translate a nucleotide (DNA/RNA) sequence to a protein sequence ExPASy Translate.