 It has been suggested that the major impediment to quality model production is inadequacies in sequence alignment, since "optimal" structural alignments between two proteins of known structure can be used as input to current modeling methods to produce quite accurate reproductions of the original experimental structure.Attempts have been made to improve the accuracy of homology models built with existing methods by subjecting them to molecular dynamics simulation in an effort to improve their RMSD to the experimental structure.However, current force field parameterizations may not be sufficiently accurate for this task, since homology models used as starting structures for molecular dynamics tend to produce slightly worse structures.