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A protein structural alphabet and its substitution matrix CLESUM

Wei-Mou Zheng·Xin Liu
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Abstract

By using a mixture model for the density distribution of the three pseudobond angles formed by $C_α$ 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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Wei-Mou Zheng, Xin Liu. 2004-12-28. A protein structural alphabet and its substitution matrix CLESUM. https://arxiv.org/abs/q-bio/0412046

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