Menu Features
  • Home (first page) dislays the basic information about the web tool and current development status.
  • Run CUPSAT provides links to two modules: the basic module (prediction from PDB structures) and prediction from custom developed structures.
  • Server status gives the online status of CUPSAT server and the local PDB mirror.
  • Concise documentation is provided for the modules in Help menu.
  • Send us your feedback. Contact details are provided.

Predict Mutant Stability from PDB Structures (Basic Module)
  • This module predicts stabilty changes upon point mutation from a PDB structure.
  • This is available from: Run CUPSAT > Predict Mutant Stability from Existing PDB structures.
  • Initially, given PDB file is analysed for ita atom environment & secondary structure features.
  • Details of Accessible Surface Area & Secondary structure specificity of the given amino acid environment are provided (DSSP).
  • Torsion angle information is provided.
  • Input details: PDB ID, Wild type anino acid, mutant amino acid, residue ID. chaind id may be required.
  • Some PDB structures either don't have chain specification or have only one chain. In that case, the program doesn't require chain ID. If there are multiple chains and the supplied wild type amino acid and residue ID match only one chain, the program assumes that the input belongs to a specific chain. All others cases require chain ID to be selected. The program gives comprehensive information about the structure and stability in the next screens.

Predict Mutant Stability from Custom Protein Structures
  • This module predicts stabilty changes upon point mutation from a custom developed protein structure
  • Any structure that is not available from PDB can be uploaded and used.
  • The protein structure must be formatted according to PDB file formats guide.
  • NMR structures may have multiple alternative models in the same PDB file for a specific protein. These models are similar to each other. The basic module takes the first model from PDB for prediction (using the MODEL-ENDMDL tags). If you like to use an alternative model, extract the model (copy and paste from MODEL to ENDMDL) to a new file and use this module.
  • Once the upload is complete, file details are shown in the next screen. Upon confirmation, click Proceed to continue. The rest of process is similar to the basic module.