How to use PremPS Server?

Step 1 - Provide a protein structure

You can either input the PDB code, the structure will be retrieved from the Protein Data Bank, or upload your own structure file, which must comply with the PDB format.

In either case, the structure file should contain at least one protein chain. Please note that:

If a valid PDB code is input, the title of the PDB will be shown.

Step 2 - Define chains for calculating protein stability change

A user can choose chains by clicking on the button of any chain thumbnail.

Step 3 - Select mutations to estimate their effects on protein stability

Three options are provided for user to select mutations: "Specify One or More Mutations Manually" , "Upload Mutation List" and "Alanine Scanning for Each Chain"


Upon the completion of the third step and submission of the job, PremPS provides a job identifier for checking the job status, an estimate of “Expected processing time”, and the “Job start time”. If an e-mail address is provided, the link to the results page will be sent via e-mail. The results will be available on this page as soon as the calculations are done. The example below shows precalculated results for job 2020060501421741365460632.

For each job, PremPS presents a summary and actual processing time. For each mutation, the following results are provided:

Browser compatibility

OS Version Chrome FireFox Mircosoft Edge Safari
Linux CentOS7 not tested 60.6 n/a n/a
MacOS 10.14 78.0 70.0 n/a 12.0.3
Windows 10 78.0 56.0b3 44.1 n/a

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