Structure comparison opens a window into the distant past of protein evolution, which has
been unreachable by sequence comparison alone. With 55000 entries in the Protein Data …

The identification of geometric relationships between protein structures offers a powerful
approach to predicting the structure and function of proteins. Methods to detect such …

This paper discusses certain modifications of the ideas concerning the Gromov–Hausdorff
distance which have the goal of modeling and tackling the practical problems of object …

This book is the first easy-to-read text on nonsmooth optimization (NSO, not necessarily
differentiable optimization). Solving these kinds of problems plays a critical role in many …

We report the largest and most comprehensive comparison of protein structural alignment
methods. Specifically, we evaluate six publicly available structure alignment programs …

Even when there is agreement on what measure a protein multiple structure alignment
should be optimizing, finding the optimal alignment is computationally prohibitive. One …

The Dali program is widely used for carrying out automatic comparisons of protein structures
determined by X‐ray crystallography or NMR. The most familiar version is the Dali server …

Proteins are the most essential and versatile macromolecules of life, and the knowledge of
their functions is a crucial link in the development of new drugs, better crops, and even the …

Motivation: Existing comparisons of protein structures are not able to describe structural
divergence and flexibility in the structures being compared because they focus on identifying …

In the fifty years since the first atomic structure of a protein was revealed, tens of thousands
of additional structures have been solved. Like all objects in biology, proteins structures …