MODPEP -- fast ab initio structure prediction of linear peptides or disorder proteins

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Help for using MODPEP server

1. How to provide input for a peptide.

The MODPEP server is to generate the conformation of protein-bound peptides. It is designed to be easily used. The only input for users to provide is just the peptide sequence. The MODPEP server can accept two types of input for the peptide to be modeled:

Only ONE type of input is needed for a peptide.

If more than one type of input are provided, the first one will be used. The maximum number of peptide conformations to be generated is 1000 and this number is 100 by default.

Refinement: The server also offers users an option to refine the generated peptide conformations by a short MD simulation. If selecting "Yes", the job will take minutes instead of seconds to model 100 peptide conformations, and the result package will include the refined peptide models instead of the initially generated conformations.

2.How to obtain the results after submitting the job.

After users provide the peptide sequence and submit the job to our MODPEP server, the job will be put in queue waiting to be run on our system. Users will also be redicted to the results page which will be refreshed every 10 seconds until the results are shown on the page.

Since MODPEP is very fast, users can normally obtain the results within seconds or minutes depending on the length of the peptide to be modeled. If users don't want to wait for the results, they can bookmark the results page and come back later to view and download the results.

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