Using Domain-Based Structural Ensemble to Improve Structure Modeling

In this paper, we presented a method to improve structural modeling based on conserved domain clusters and structure-anchored alignment. First we mapped all the InterPro domains in the entire PDB, partitioned and clustered homologous domains into the domain-based template library. This aimed at expanding structural coverage to more protein sequences. For each cluster, we generated a multiple structural alignment based only on the 3 D information. Then we extracted a core-structure and built a position-specific profile from the structure and sequence information for each of cluster. Based on the multiple structural alignments, core-structures and the profiles, we developed a structure-anchored alignment method to increase the alignment accuracy between a query and its templates. Preliminary results show that our template library and the structure-anchored alignment method can be used for the prediction for a majority of known protein sequences with better qualities.