As a fundamental problem in computational structure biology, protein structure alignment
has attracted the focus of the community for more than 20 years. While the pairwise structure …

Although the universe of protein structures is vast, these innumerable structures can be
categorized into a finite number of folds. New functions commonly evolve by elaboration of …

The evolution and diversification of different types of photosynthetic reaction centers (RCs)
remains an important unresolved problem. We report here novel sequence features of the …

Several protein structure classification schemes exist that partition the protein universe into
structural units called folds. Yet these schemes do not discuss how these units sit relative to …

Motivation: Calculating multiple protein structure alignments (MSAs) is important for
understanding functional and evolutionary relationships between protein families, and for …

Protein structure alignment methods are used for the detection of evolutionary and
functionally related positions in proteins. A wide array of different methods are available, but …

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be
observed in loop regions, rearrangements between secondary structure elements, and …

Motivation Structures are replacing the role of sequences. Traditional bioinformatics
research focused on sequences because they were easily obtained. Advances in …

A variety of methods have been proposed for structure similarity calculation, which are
called structure alignment or superposition. One major shortcoming in current structure …

Flexible proteins are proteins that have conformational changes in their structures. Protein
flexibility analysis is critical for classifying and understanding protein functionality. For that …