![]() ![]() Select a residue to mutate to from the drop down list or select "all" to try all 20 natural amino acids. If you have selected a residue it should be reported in the "Residue to Mutate" box. Step 2 Choose the option MolMechanics/Try Mutation/ Protein Stability and a dialog box as shown above will be displayed. Step 1 Read in the PDB file of interest and select the residue you wish to mutate. A positive energy value indicates that the mutation is likely to be destabilizing. ![]() The rest of the protein structure is considered rigid. Mutation of a given residue is followed by Monte Carlo simulations with flexible side chains for the mutated residue and its neighboring residues. The residue-specific energies were derived empirically using a large set of experimental data. The free energy change in protein stability is computed as follows:ĬalculationThe free energy of the unfolded and misfolded states is approximated by a sum of the residue-specific energies. "Scan Sequence" allows you to mutate all the residues in the sequence to the specified amino acid. A graphical selection of the residue to be mutated is then made, the mutant amino acid (e.g., "ala" or "all" for calculation of the energy for all natural amino acids) is then selected. Getting Started: A PDB structure or ICM object containing the protein complex is needed. ![]() This method computes the change in protein stability upon mutation of a single residue. 9.13 Predicting Change in Protein Stability upon MutationĪvailable in the following product(s): ICM-Pro ![]()
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