Discrete representations of the protein Ca chain

Background: When a large number of protein conformations are generated and screened, as in protein structure prediction studies, it is often advantageous to change the conformation in units of four consecutive residues at a time. The internal geometry of a chain of four consecutive Ca atoms is completely described by means of the three angles u1, t, and u2, where t is the virtual torsion angle defined by the four atoms and u1 and u2 are the virtual bond angles flanking the torsion angle on either side. In this paper, we examine the quality of the protein structures that can be obtained when they are represented by means of a set of discrete values for these angles (discrete states).