is there any software or tool which would tell us the activity of peptide from the amino acid sequence??
Dear Madhura,
There are a number of tools available, so it very much depends on what you want and what you are looking for. Some ideas you could try are:
The Antimicrobial Peptide Database (APD), this will give you an idea about the potential antimicrobial activity:
https://www.researchgate.net/publication/8955074_APD_the_Antimicrobial_Peptide_Database
See for searchable website corresponding to this database:
http://aps.unmc.edu/AP/main.php
It is as far as I can judge, THE most comprehensive database when it comes to antimicrobial peptides.
If you are interested in the general characteristics several tools are available:
For a secondary structure prediction several tools are available:
http://bioinf.cs.ucl.ac.uk/psipred/
https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html
http://helios.princeton.edu/CONCORD/
For an idea about the membrane affinity potential several tools are available:
Heliquest: One of its features is the so-called lipid discrimination factor. It tells you whether a sequence (typically 18 AA long) is a potential lipid binding region or not.
https://www.researchgate.net/publication/23133533_HELIQUEST_A_web_server_to_screen_sequences_with_specific_a-helical_properties
See following reference for example:
https://www.researchgate.net/publication/47460373_The_prediction_of_novel_multiple_lipid-binding_regions_in_protein_translocation_motor_proteins_A_possible_general_feature
Eisenberg plot approach: Allows you to dissect on whether a sequence is a transmembrane or amphiphilic helix or presumably part of a soluble/globular protein.
https://www.researchgate.net/publication/16693014_Analysis_of_Membrane_and_Surface_Protein_Sequences_with_the_Hydrophobic_Moment_Plot
Or its related Heliquest based Eisenberg plot approach: Similar features as the original hydrophobic moment plot approach by Eisenberg but easy to use (and reproducible).
https://www.researchgate.net/publication/51733310_New_User-Friendly_Approach_to_Obtain_an_Eisenberg_Plot_and_Its_Use_as_a_Practical_Tool_in_Protein_Sequence_Analysis
See following references for examples:
https://www.researchgate.net/publication/230825800_Prediction_of_Lipid-Binding_Regions_in_Cytoplasmic_and_Extracellular_Loops_of_Membrane_Proteins_as_Exemplified_by_Protein_Translocation_Membrane_Proteins
https://www.sciencedirect.com/science/article/pii/S0005273614004507
MCPep: A Monte-Carlo approach (with a user-friendly webserver facility) that allows you to see whether a peptide has an affinity for lipid membranes and whether the peptide is bound in a surface or transmembrane kind of fashion.
https://www.researchgate.net/publication/225307205_Monte_Carlo_simulations_of_peptide-membrane_interactions_with_the_MCPep_web_server
See following reference for example:
https://www.researchgate.net/publication/268881276_Identification_and_in_silico_analysis_of_helical_lipid_binding_regions_in_proteins_belonging_to_the_amphitropic_protein_family
Possibly the following reference is of any relevance to you when you are interested in the half-life of your peptide. Called PEPLife:
http://crdd.osdd.net/raghava/peplife/
Select the download option and subsequently reference:
http://crdd.osdd.net/raghava/peplife/ref.php
Hope this helps you any further and will give you, after a full bioinformatics characterization, directions towards further experimentation.
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