Determining the structural properties of mRNA is key to understanding vital post-transcriptional processes. As experimental data on mRNA structure are scarce, accurate structure prediction is required to characterize RNA regulatory mechanisms. Although various structure prediction approaches are available, it is often unclear which to choose and how to set their parameters. Furthermore, no stan...

Chemists working in biomolecular application projects are usually looking at many related molecules (e.g. results of a virtual screening run, lead series development or library design). For a convenient visual analysis of this data it is essential that differences between molecules are easily detectable. This can be quite difficult if structural similarities are not taken into account while cre...

MOTIVATION Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired ar...

The local geometry of a DNA helix can influence protein recognition, but the sequence-specific features that contribute to helix structure are not fully understood, and even less is known about how RNA helix geometry may affect protein recognition. To begin to understand how local or global helix structure may influence binding in an RNA model system, we generated a series of DNA analogues of H...

This paper investigates the problem of finding subclasses of nonmonotonic reasoning which can be implemented efficiently. The ability to “define” propositions using default assumptions about the same propositions is identified as a major source of computational complexity in nonmonotonic reasoning. If such constructs are not allowed, i.e. stratified knowledge bases are considered, a significant...

In this paper we study the log structures on generalized semistable varieties, generalize the result by F. Kato and M. Olsson, and prove the canonicity of log structure when it can be expected. In out text we first give the definitions of local chart and weakly normal crossing morphism. Then we study the invariants of complete noetherian local ring coming from weakly normal crossing morphisms. ...

In many studies, the alternative load path method (APM) has been used for progressive collapse analysis. In this method, one or several columns of the building are removed and the building response is investigated. This method ignores the initial local failure cause of building and this can affect the structural response. Investigation of ignoring the initial local failure cause of steel braced...

RNA sequences fold upon themselves to form complex structures. Functional analysis of most biological RNAs requires knowledge of secondary structure arrangements and tertiary base interactions. Therefore, rapid and comprehensive methods for assessing RNA structure are highly desirable. Computational tools are oftentimes employed for prediction of secondary structure. However, a greater degree o...