Alignment Analysis
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Structural and cell biology studies often require engineering proteins with enhanced solubility. This server identifies solvent exposed hydrophobic residues in a protein sequence, and compares them with those of closely related sequences, providing thus useful help to select the best residues to be targeted for site-directed mutagenesis.

Note: Altering solvent exposed surface residues can result in loss of the biological function of a protein. Therefore, the information generated by this tool should be complemented with any available experimental data.

These are the steps followed by the server:
  • 1. Models the 3D-structure the of input sequence (query). Models are produced by SCWRL, using a template obtained from a PSI-BLAST search against the PDB database. Model is only built only if the e-value of the sequence template is < 1e-5. If the template identity to the query is > 95% following calculations are carried out over the template. Insertions and deletions are not modeled in this version of the program

  • 2. Calculates the Fractional Solvent accessibility of the models using NACCESS

  • 3. Outputs a 3D-model of the query, and a multiple sequence alignment of the query and various close orthologues.

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