Jun 28 2018
| Tutorial |
This method computes the change in protein stability upon mutation of a single residue.
Getting Started: A PDB structure or ICM object containing the protein complex is needed. 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.. "Scan Sequence" allows you to mutate all the residues in the sequence to the specified amino acid.
The free energy change in protein stability is computed as follows:
CalculationThe free energy of the unfolded and misfolded states is approximated by a sum of the residue-specific energies. The residue-specific energies were derived empirically using a large set of experimental data. Mutation of a given residue is followed by Monte Carlo simulations with flexible side chains for the mutated residue and its neighboring residues. The rest of the protein structure is considered rigid. A positive energy value indicates that the mutation is likely to be destabilizing.
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