Molecular modeling in protein design and engineering

The graphics, energy minimization, and molecular dynamics simulations of the proteins are discussed. They were carried out using QUANTA/CHARMm graphics and molecular mechanics modeling programs. The molecular mechanics and dynamics calculations included terms for bond stretching, bond angle bending, torsional potentials, improper out-of-plane forces, electrostatic Coulombic forces, and van der Waals interactions for all atom-atom interactions in the proteins, and water interaction terms for solvation effects where solvent was included. Problems encountered in protein engineering are described.<>