ALPHASUM: a score matrix based on low identity all-alpha proteins

Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological research. However, alignment in "Twilight Zone" is still a challenging issue. New score matrices such as Position Specific Score Matrix and structural context-based matrix have been issued to deal with it, whereas generalized matrices are still useful in pairwise alignment and/or some steps of generating profiles. Family-specific matrices have been proved effective in improving alignment, whereas the generalization of them is reduced. ALPHASUM, a score matrix based on structure alignment of low identity all-alpha proteins is constructed. Performance comparison suggests substitution pattern difference between all-alpha proteins and all proteins and indicates that alignment of all-alpha proteins in "Twilight Zone" can be improved by using alpha class-specific matrix and gap penalties. The implication between structure-derived matrix and influence of amino acid substitution to structure is also suggested.