APD3 - AMP tools

Additional Tools for Antimicrobial Peptides (updated Jan 2024)

There are additional tools for antimicrobial peptide research and education, which can accessed via the following links.

1. Predict antimicrobial peptides by machine learning

You can try select prediction tools in the APD Links. Machine learning predicted and experiment-validated sequences are collected in the APD as a new peptide group.

2. Predict the cleavage sites of signal peptides

You can use the 2022 new version SignalP-6.0.

3. Identify known 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. Multiple peptide sequence alignment

A set of alingment programs are available for this purpose.

You can do the multiple sequence alignment of either polypeptides or nucleic acids using ClustalW2.

5. Molecular evolutionary genetics analysis (MEGA) tool: How to build a phylogenetic tree for sequences?

You can analyze the evolutional relationship of thousands of AMP sequences using MEGA11.

6. Translate tool

You can translate a nucleotide (DNA/RNA) sequence to a protein sequence ExPASy Translate.

7. Peptide helical wheel, hydrophobicity and hydrophobic moment

You can figure it out here.

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. 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.

11. 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.

12. Peptide isoelectric point pI, estimated half life, instability index and aliphatic index calculations

All these parameters can be calculated here ExPASy.

13. ProScale: Amino acid property profiles for peptides

A variety of peptide profiles can be generated using ProtScale. It can be any property (molecualr weight, bulkiness, polarity, recognition factors, HPLC retention time, helix, and so on). It provides information for each amino acid. For instance, a hydrophobic scale plot enables you to see the amphipathicity pattern of the sequence.

14. Peptide stability: predict the potential cleavage sites by proteases or chemicals

You can use PeptideCutter

15. Peptide half life in intestine-like environment

It can be estimated using the HLP tool.

16. Peptide cell penetrating ability

This ability can be determined by CellPPD tool.

17. Peptide antigenicity, allergic potential and toxicity

This ability can be determined by antigenic prediction.

18. HPLC retention time prediction

You can predict it using Retention Prediction Server.

19. Peptide/Protein secondary structure prediction

You may predict the secondary structure of AMPs using PSIPRED.

20. Full chain protein tertiary 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.

21. Artificial intelligence (AI) protein structure prediction

AlphaFold 2 freely available.

22. Circular dichroism (CD) data analysis

You can analyze your CD data here.

23. Heterologous recombinant expression of antimicrobial peptides

You can optimize the codon for your peptide production using DNAWorks. You can optimize the codons for expression hosts, including E. coli, S. cerevesiae, C. elegans, D. melanogaster, P. pastoris, H. sapiens, R. norvegicus, X. laevis, and M. musculus.
Last updated: Jan 2024 | Copyright 2003-2024 Dept of Pathology, Microbiology & Immunology, UNMC All Rights Reserved