I am interested in finding some bioinformatics tools to study how peptides could interact with the cell membrane and what the outcome of this interaction could be. Please help in this regard.
For those (still) interested in this question I will try to answer this question.
There are a number of tools 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
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