Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection

Bin Liu, Deyuan Zhang, Ruifeng Xu, Jinghao Xu, Xiaolong Wang, Qingcai Chen, Qiwen Dong, Kuo-Chen Chou

Abstract: Owing to its importance in both basic research (such as molecular evolution and protein attribute prediction) and practical application (such as timely modeling the 3D structures of proteins targeted for drug development), protein remote homology detection has attracted a great deal of interest. It is intriguing to note that the profile-based approach is promising and holds high potential in this regard. To further improve protein remote homology detection, a key step is how to find an optimal means to extract the evolutionary information into the profiles.