Identifying functional motifs on protein surfaces by structural alignment with sequence information

Protein local structures, especially the regional patterns of surface cavities, are critical to determine specific protein functions and crucial in drug design and other protein engineering [1, 2]. It is in pressing need to develop novel structural alignment methods to identify these functional structural motifs. Although many structure alignment methods have been developed [3], most of them require the implicitly incorporation of sequence order constraints, which may suit for revealing global similarity between whole structures but fails to detect local structure similarity since it not only sacrifices the accuracy of the result, but also increases the difficulty and loses the biochemical similarity implication [4]. In this paper, we propose a new method to identify functional motifs on protein surface cavities by combining sequence and structure information together in protein local structure alignment. We believe that involvement of sequence information in structure alignment may generate more robust and biologically meaningful results.