A protein structural alphabet and its substitution matrix CLESUM

Details A protein structural alphabet and its substitution matrix CLESUM A protein structural alphabet and its substitution matrix CLESUM

2004-12-28

arxiv.org/abs/q-bio/0412046v1

Biology

Quantitative Biology

Biomolecules

10 pages

Scientific paper

By using a mixture model for the density distribution of the three pseudobond angles formed by $C_\alpha$ atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural alphabet. This coarse-graining procedure converts a 3D structure to a 1D code sequence. A substitution matrix between these letters is constructed based on the structural alignments of the FSSP database.

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