has input has output Sequence-structure alignment Protein structure Protein threading Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. Align molecular sequence to structure in 3D space (threading). Sequence-to-3D-profile alignment Sequence-structure alignment beta12orEarlier This includes sequence-to-3D-profile alignment methods, which align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment) - methods might perform one-to-one, one-to-many or many-to-many comparisons. Sequence-3D profile alignment Fold recognition