Improving protein secondary structure prediction based on short subsequences with local structure similarity

BMC Genomics

Table 7 The relationship between the number of distinct synonymous words and the prediction performance.

Selection criterion		e≥0	e≥5	e≥25	e≥50	e≥75	e≥100	e≥125	e≥150
Number of selected proteins		8297	7983	7252	6660	6178	5637	5035	4378
Q ₃	SymPred	81.0	81.6	82.3	82.8	83.1	83.3	83.4	83.5
SymPsiPred	83.9	84.3	84.8	85.1	85.2	85.3	85.4	85.5

For each test protein t of length L in DsspNr-25, let v denote the number of distinct synonymous words of t. Define e = v/L, the multiplicity of v over L. If e is greater than or equal to a threshold, the protein t is selected. The results show that there is a positive correlation between the number of distinct synonymous words and the prediction performance of SymPred and SymPsiPred.

ISSN: 1471-2164