Protein secondary structure prediction using sequence profile and conserved domain profile

In this paper, we proposed a novel method for protein secondary structure prediction using sequence profile and conserved domain profile. Sequence profile generated from PSI-BLAST (position specific iterated BLAST) has been widely used in protein secondary structure prediction, because PSI-BLAST shows good performance in finding remote homology. Conserved domains kept functional and structural information of related proteins; therefore we could draw remote homology information in conserved domains using RPS-BLAST (reverse position specific BLAST). We combined sequence profile and conserved domain profile to get more remote homology information, and propose a method which used the combined profile to predict the protein secondary structures. In order to verify the effectiveness of our proposed method, we implemented a protein secondary structure prediction system. Overall prediction accuracy reached 75.9% on the RS126 data set. The improvement by incorporating conserved domain information exceeded 3%, and this result showed that our proposed method could improve significantly the accuracy of protein secondary structure prediction.