- Perform the CASTp analysis on different kinds of HIV proteases to analyse its surface features. Give an account of the pockets and cavities, along with the measurements.
- Analyse some of the bacterial membrane proteins of Escherichia coli such as, 2O9D, 2O9E, 2O9F, 2O9G, 1QFG, 1QJ8 and 1QJ9 (available in Protein Data Bank) usig CASTp. CASTp identifies all pockets and cavities of the protein. Locate the pockets and cavities on these proteins and measure their volume and area (using CASTp). Also find out the number, area, and circumcircle of the mouth openings for each pocket. Compare the solvent accessible surface (SA, Richards' surface) and the molecular surface (MS, Connolly's surface). In addition to this, get the pocket information file, pocket atoms and mouth atoms from the emailed result.
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