A global optimization method is described for identifying the global minimum energy conformation, as well as lower and upper bounds on the global minimum conformer of solvated peptides. Potential energy contributions are calculated using the ECEPP/3 force field model. In considering the effects of hydration, two implicit free energy models are compared. One method is based on the calculation of solvent-accessible surface areas, while the other uses information on the solvent-accessible volume of hydration shells. Detailed information on the potential and solvation energy contributions is presented for the terminally blocked single residue peptides. In addition, based on a procedure that allows the exclusion of domains of the (φ, ψ) space, a number of oligopeptide structure prediction problems are considered, and the role of the solvation model in defining global minimum conformations is addressed.
All Science Journal Classification (ASJC) codes
- Chemical Engineering(all)
- Computer Science Applications
- Global optimization
- Protein folding