Protein secondary structure prediction for a single-sequence using hidden semi-Markov models

Aydin, Zafer; Altunbasak, Yucel; Borodovsky, Mark

doi:10.1186/1471-2105-7-178

BMC Bioinformatics

Table 7 Positional dependencies within structural segments for the models $ℳ$ 1, $ℳ$ 2, and $ℳ$ 3. $h_{j}^{3}$ ∈ {hydrophobic, neutral, hydrohilic} indicates the hydrophobicity class of the amino acid R_j, where hydrophobic = {A, M, C, F, L, V, I}, neutral = {P, Y, W, S, T, G}, hydrophilic = {R, K, N, D, Q, E, H}. $h_{j}^{5}$ is a 5 letter alphabet with groups defined as {P, G}, {E, K, R, Q}, {D, S, N, T, H, C}, {I, V, W, Y, F}, {A, L, M}.

From: Protein secondary structure prediction for a single-sequence using hidden semi-Markov models

		$ℳ$ 1	$ℳ$ 2	$ℳ$ 3
H	Int	$h_{i - 2}^{5}, h_{i - 3}^{3}, h_{i - 4}^{5}, h_{i - 7}^{3}$	$h_{i - 2}^{3}, h_{i - 3}^{3}, h_{i - 4}^{3}, h_{i + 2}^{3}, h_{i + 4}^{3}$	$h_{i + 2}^{5}, h_{i + 3}^{5}, h_{i + 4}^{5}$
	N1	$h_{i - 1}^{5}, h_{i - 2}^{5}$	$h_{i - 1}^{5}, h_{i + 2}^{5}$	$h_{i + 2}^{5}, h_{i + 4}^{5}$
	N2	$h_{i - 1}^{3}, h_{i - 2}^{3}, h_{i - 3}^{3}$	$h_{i - 2}^{3}, h_{i + 2}^{3}, h_{i + 4}^{3}$	$h_{i + 1}^{3}, h_{i + 2}^{3}, h_{i + 4}^{3}$
	N3	$h_{i - 1}^{3}, h_{i - 2}^{3}, h_{i - 3}^{3}$	$h_{i - 2}^{3}, h_{i - 3}^{3}, h_{i + 2}^{3}$	$h_{i + 1}^{3}, h_{i + 2}^{3}, h_{i + 4}^{3}$
	N4	$h_{i - 1}^{3}, h_{i - 2}^{3}, h_{i - 3}^{3}$	$h_{i - 1}^{3}, h_{i + 2}^{3}, h_{i + 4}^{3}$	$h_{i + 1}^{3}, h_{i + 2}^{3}, h_{i + 4}^{3}$
	C1	$h_{i - 1}^{3}, h_{i - 2}^{3}, h_{i - 4}^{3}$	$h_{i - 2}^{3}, h_{i - 4}^{3}, h_{i + 1}^{3}$	$h_{i + 1}^{3}, h_{i + 2}^{3}, h_{i + 3}^{3}$
	C2	$h_{i - 2}^{3}, h_{i - 3}^{3}, h_{i - 4}^{3}$	$h_{i - 2}^{3}, h_{i - 4}^{3}, h_{i + 1}^{3}$	$h_{i + 1}^{3}, h_{i + 2}^{3}, h_{i + 3}^{3}$
E	Int	$h_{i - 1}^{5}, h_{i - 2}^{5}, h_{i - 3}^{3}$	$h_{i - 1}^{3}, h_{i - 2}^{3}, h_{i + 1}^{3}, h_{i + 2}^{3}$	$h_{i + 1}^{5}, h_{i + 2}^{5}, h_{i + 3}^{3}$
	N1	$h_{i - 1}^{5}, h_{i - 2}^{5}$	$h_{i - 1}^{5}, h_{i + 1}^{5}$	$h_{i + 1}^{5}, h_{i + 2}^{5}$
	N2	$h_{i - 1}^{5}, h_{i - 2}^{5}$	$h_{i - 1}^{5}, h_{i + 2}^{5}$	$h_{i + 1}^{5}, h_{i + 2}^{5}$
	C1	$h_{i - 1}^{3}, h_{i - 3}^{3}, h_{i - 4}^{3}$	$h_{i - 1}^{3}, h_{i - 3}^{3}, h_{i + 1}^{3}$	$h_{i + 1}^{3}, h_{i + 2}^{3}, h_{i + 3}^{3}$
	C2	$h_{i - 1}^{5}, h_{i - 2}^{5}$	$h_{i - 1}^{5}, h_{i + 1}^{5}$	$h_{i + 1}^{5}, h_{i + 2}^{5}$
L	Int	$h_{i - 1}^{5}, h_{i - 2}^{5}, h_{i - 3}^{3}, h_{i - 4}^{3}$	$h_{i - 1}^{5}, h_{i - 2}^{3}, h_{i + 1}^{5}, h_{i + 2}^{3}$	$h_{i + 1}^{5}, h_{i + 2}^{5}, h_{i + 3}^{3}, h_{i + 4}^{3}$
	N1	$h_{i - 1}^{5}, h_{i - 2}^{5}, h_{i - 3}^{3}$	$h_{i - 1}^{5}, h_{i - 2}^{5}, h_{i + 1}^{3}$	$h_{i + 1}^{5}, h_{i + 2}^{5}, h_{i + 3}^{3}$
	N2	$h_{i - 1}^{5}, h_{i - 2}^{3}, h_{i - 4}^{3}$	$h_{i - 1}^{5}, h_{i - 2}^{3}, h_{i + 1}^{3}$	$h_{i + 1}^{5}, h_{i + 2}^{3}, h_{i + 4}^{3}$
	N3	$h_{i - 1}^{5}, h_{i - 2}^{3}, h_{i - 3}^{3}$	$h_{i - 1}^{5}, h_{i - 2}^{3}, h_{i + 1}^{3}$	$h_{i + 1}^{5}, h_{i + 2}^{3}, h_{i + 3}^{3}$
	N4	$h_{i - 1}^{5}, h_{i - 2}^{3}, h_{i - 3}^{3}$	$h_{i - 1}^{5}, h_{i - 2}^{3}, h_{i + 1}^{3}$	$h_{i + 1}^{5}, h_{i + 2}^{3}, h_{i + 3}^{3}$
	C1	$h_{i - 1}^{5}, h_{i - 2}^{5}, h_{i - 3}^{3}$	$h_{i - 1}^{5}, h_{i - 2}^{5}, h_{i + 1}^{3}$	$h_{i + 1}^{5}, h_{i + 2}^{5}, h_{i + 3}^{3}$
	C2	$h_{i - 1}^{5}, h_{i - 2}^{5}$	$h_{i - 1}^{5}, h_{i + 3}^{5}$	$h_{i + 1}^{5}, h_{i + 2}^{5}$
	C3	$h_{i - 1}^{3}, h_{i - 2}^{3}, h_{i - 3}^{3}$	$h_{i - 1}^{3}, h_{i + 1}^{3}, h_{i + 2}^{3}$	$h_{i + 1}^{3}, h_{i + 2}^{3}, h_{i + 3}^{3}$
	C4	$h_{i - 1}^{3}, h_{i - 2}^{3}, h_{i - 3}^{3}$	$h_{i - 2}^{3}, h_{i - 3}^{3}, h_{i + 1}^{3}$	$h_{i + 1}^{3}, h_{i + 2}^{3}, h_{i + 3}^{3}$

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ISSN: 1471-2105

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