Background: Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved ...
: We introduce the novel concept of graph alignment, a generalization of graph isomorphism that is motivated by the commonly used multiple sequence alignments. Graph alignments and...
Background: Detection of common evolutionary origin (homology) is a primary means of inferring protein structure and function. At present, comparison of protein families represent...
The protein-protein interaction networks of even well-studied model organisms are sketchy at best, highlighting the continued need for computational methods to help direct experim...
Background: The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as `states'...