• Indirectly capture interactions among structural motifs in 3D space: In our previous work, two bit-patterns are considered spatially proximate if they are located in the same vicinity within a 2D contact map. This is problematic in the context of protein folding, as two bit-patterns can be spatially proximate in a contact map even though their corresponding motifs are distant in the 3D conformation. (See Section 3 for more details.) We address this issue by considering the 3D distance between two bit-patterns.