Hello everyone, How are you guys doing?
I'm currently working with antimicrobial peptide (AMP) project and one of our objectives is to predict the interaction of peptide against bacterial cell wall/membrane. AMP has been shown to exhibit inhibition by targeting the cell membrane. Previously, there is MCPep server to simulate the interaction but there are not active anymore. Could anyone suggest an alternative either online server/protocols so that we can simulate our peptide interaction. We are working mostly on peptide with 5-50 amino acid length. Thank you in advance.
Dear Fareed Sairi ,
As a regular user of the MCPep server I noticed (like you) that the server has been out of operation for already quite some time. I Noticed that they (not sure since when) restructured their website: https://www.bentalab.com/servers I sincerely hope that they will fix things soon.
By the way, my personal experience is that contacting the people behind this server helped (at least throughout the years it did…).
For the moment I advise you to have a look at Heliquest (https://heliquest.ipmc.cnrs.fr/ ). One of the features of this program is the prediction of the so-called “Possible Lipid-Binding Helix” (https://heliquest.ipmc.cnrs.fr/HelpProcedure.htm#heading2). See for an example about the use of this feature:
Article The prediction of novel multiple lipid-binding regions in pr...
I developed an “Heliquest based Eisenberg plot approach”:
Article New User-Friendly Approach to Obtain an Eisenberg Plot and I...
To predict lipid binding regions and classify them into transmembrane helix, amphipathic helix and (other) potential lipid binding helix, see for example:
Article Identification and in silico analysis of helical lipid bindi...
This can be a good tool for a first indication. In the last paper you can see how indeed MCPep can provide additional (and confirmative) information. Hopefully MCPep will be back soon, like you I am interested in a possible alternative fort his very useful too. For the moment I think the Heliquest program might be of use for your research.
Best regards.
Dear Fareed Sairi ,
I can recommend toolkit GROMACS https://www.gromacs.org/
With best regards.
Dear Rob Keller and Sergei Grishin, thank you for the sharing. I did contact the people behind MCPep server and they replied that the server was down for the time being until further notice. I am what people called the end-user because my background is not related to bioinformatics. I just start my journey to work with antimicrobial peptide in silico recently. Thus, both of your insights are very helpful. I will have a look at what Rob Keller had suggested and I hope everyone can help me again in the future when I have some more questions. Thank you very much.
Warm regards,
Fareed Sairi
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