The sequence-structure gap is rapidly increasing. Currently, databases for protein sequences (e.g., SWISS-PROT [1]) are expanding rapidly, largely due to large-scale genome sequencing projects: at the beginning of 1998, we know already all sequences for a dozen of entire genomes (2). This implies that despite significant improvements of structure determination techniques, the gap between the number of protein structures in public databases (PDB [3]), and the number of known protein sequences is increasing. The most successful theoretical approach to bridging this gap is homology modeling. It effectively raises the number of “known” 3D structures from 7000 to over 50,000 (4,5).