How to use PremPS Server?
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:
- Bioassembly (biological unit) is the default structure. You can choose all biological assemblies for each protein structure and the first bioassembly (.pdb1) will be used as default.
- If the structure file includes multiple NMR models, only the first one will be used in calculations.
- If the uploaded structure file includes multiple protein structures, only the first one will be considered.
- Non-protein molecules and non-standard residues are not considered during the calculations.
- PremPS chooses the first coordinate for the atom if several different coordinates are provided in the PDB file.
If a valid PDB code is input, the title of the PDB will be shown.
A user can choose chains by clicking on the button of any chain thumbnail.
- PremPS provides a 3D view of the structure colored by chains. Each chain is listed with the corresponding name of the protein.
- One can assign one chain or multiple chains but they must belong to one protein; only the selected chains will be taken into account during the calculation. In addition, selected chains must be up to 20 amino acids in length.
- For bioassemblies if any protein chain in the structure were generated by applying symmetry operations, they are depicted with the labels of alphanumeric combinations (for example, 'A_1') indicating the source molecule/chain from which they were generated.
Three options are provided for user to select mutations: "Specify One or More Mutations Manually" , "Upload Mutation List" and "Alanine Scanning for Each Chain"
- In the option of "Specify One or More Mutations Manually", the user can not only perform calculations for specified mutations but also visualize the mutated site in the wild-type protein using the 3D viewer.
- "Upload file" option allows the user to upload a list of mutations in a plain text file for batch processing.
- "Alanine Scanning": allows the user to perform 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:
- ΔΔG(kcal mol-1) predicted unfolding free energy change induced by a single mutation (positive and negative sign corresponds to destabilizing and stabilizing mutations, respectively);
- Location (COR/SUR), a residue is defined as buried in the protein core if the ratio of solvent accessible surface area of this residue in the protein and in the extended tripeptide is less than 0.2, otherwise it is located on the surface of protein;
Structure, PremPS provides an interactive 3D viewer showing the non-covalent interactions between the mutated site and its adjacent residues in the wild-type and mutant structure respectively, generated with Arpeggio. The example below shows the non-covalent interactions between the mutated site in the myoglobin (PDB ID: 1U7S, mutation: L104D) and its adjacent residues in the wild-type (left) and mutant (right) structure respectively.
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