Estimating the significance of sequence order in protein secondary structure prediction.

Abstract

Motivation: How critical is the sequence order information in predicting protein secondary structure segments? We tried to get a rough insight on it from a theoretical approach using both a prediction algorithm and structural fragments from Protein Databank (PDB). Results: Using reverse protein sequences and PDB structural fragments, we theoretically estimated the significance of the order for protein secondary structure and prediction. On average: (1) 79% of protein sequence segments resulted in the same prediction in both normal and reverse directions, which indicated a relatively high conservation of secondary structure propensity in the reverse direction; (2) the reversed sequence prediction alone performed less accurately than the normal forward sequence prediction, but comparably high (2% difference); (3) the commonly predicted regions showed a slightly higher prediction accuracy (4%) than the normal sequences prediction; and (4) structural fragments which have counterparts in reverse direction in the same protein showed a comparable degree of secondary structure conservation (73% identity with reversed structures on average for pentamers).