Energy-based fold recognition methods, based on the "thermodynamic hypothesis": the native conformation of a protein corresponds to a global free energy minimum of the protein/solvent system.
Score of alignments in a sequence-based comparison is local. Energy-based scores are not local. Alignment with nonlocal functions is an NP-complete problem.
Solutions: to use an alignment technique that could work with nonlocal scoring functions (computational expensive), two-level dynamic programming to optimize interacting partners for each possible pair of aligned residues, and other energy calculations that allows the use of dynamic progrmming.