PREDICTION OF PROTEIN-NUCLEIC ACID INTERACTIONS
The specific recognition of nucleic acid sequences by nucleic acid binding proteins is of critical importance to the biological function of every living species. As a result, the phenomena responsible for this recognition process have long been of considerable interest to scientists. Beginning with the pioneering work of Seeman, research into sequence-specific DNA recognition focused on the search for a “recognition code”—a collection of simple rules that would pair particular amino acids to specific bases (Seeman, Rosenberg, and Rich, 1976). However, it was soon realized that any recognition code would degenerate (Pabo and Sauer, 1984) and a general “code” may not exist at all (Matthews, 1988; Pabo and Nekludova, 2000) (Chapter 12).
Given that a sequence-based recognition code appears increasingly unlikely, the key to understanding the process of protein-DNA and protein-RNA recognition lies in the structural, physical, and chemical details of the molecular interactions themselves; these structural mechanisms have received renewed attention with the increased availability of high-resolution structures for protein/nucleic acid complexes. Computational studies of these structures have classified their interactions (Luscombe et al., 2000), describing features of their binding sites (Jones et al., 1999; Jones et al., 2001; Luscombe, Laskowski, and Thornton, 2001) and the evolutionary ...