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 …

DALI is a popular resource for comparing protein structures. The software is based on
distance‐matrix alignment. The associated web server provides tools to navigate, integrate …

Highlights•Application of computational tools from an experimentalist's perspective.•Enzyme
engineering for industrial applications supported by computational predictions.•Creation of …

The computational detection of similarities between protein 3D structures has become an
indispensable tool for the detection of homologous relationships, the classification of protein …

Protein structure alignment is a fundamental problem in computational structure biology.
Many programs have been developed for automatic protein structure alignment, but most of …

Functional prediction of carbohydrate-active enzymes is difficult due to low sequence
identity. However, similar enzymes often share a few short motifs, eg, around the active site …

Motivation Multiple sequence alignment programs have proved to be very useful and have
already been evaluated in the literature yet not alignment programs based on structure or …

Background Protein pairs that have the same secondary structure packing arrangement but
have different topologies have attracted much attention in terms of both evolution and …

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 …

Background Many functional proteins have a symmetric structure. Most of these are
multimeric complexes, which are made of non-symmetric monomers arranged in a …