Motivation: Since the whole genome sequences for many species are currently available, computational predictions of RNA secondary structures and computational identifications of t...
Background: To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of...
Background: Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed...
Background: Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary...
— Analysis of conformational changes is one of the keys to the understanding of protein functions and interactions. For the analysis, we often compare two protein structures, tak...