DIAL (dihedral alignment) is a web server that provides public access to a new dynamic
programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves …

Abstract We present MASS (Multiple Alignment by Secondary Structures), a novel highly
efficient method for structural alignment of multiple protein molecules and detection of …

Abstractt Clustering is the task of organizing a set of objects into meaningful groups. These
groups can be disjoint, overlapping, or organized in some hierarchical fashion. The key …

Despite many experimental and computational studies of the gating transition of pentameric
ligand-gated ion channels (pLGICs), the structural basis of how ligand binding couples to …

Protein structure alignment has become an important strategy by which to identify
evolutionary relationships between protein sequences. Several alignment tools are currently …

A prerequisite to understand cell functioning on the system level is the knowledge of three-
dimensional protein structures that mediate biochemical interactions. The explosion in the …

In the past years, much effort has been put on the development of new methodologies and
algorithms for the prediction of protein secondary and tertiary structures from (sequence) …

Three-dimensional protein structures are invaluable sources of information for the functional
annotation of protein molecules. These structures are best determined by experimental …

In this article we present a review of the methods used for comparing and classifying protein
structures. We discuss the hierarchies and populations of fold groups and evolutionary …

The role of structure and dynamics in mechanisms for RNA becomes increasingly important.
Computational approaches using simple dynamics models have been successful at …