Structural comparison reveals remote homology that often fails to be detected by sequence
comparison. The DALI web server (http://ekhidna2. biocenter. helsinki. fi/dali) is a platform …

The process of designing biomolecules, in particular proteins, is witnessing a rapid change
in available tooling and approaches, moving from design through physicochemical force …

In the medical, environmental, and biotechnological fields, microbial communities have
attracted much attention due to their roles and numerous possible applications. The study of …

Bacteria colonize every niche on Earth and play key roles in many environmental and host-
associated processes. The sequencing revolution revealed the remarkable bacterial genetic …

Background Protein annotation is a major goal in molecular biology, yet experimentally
determined knowledge is typically limited to a few model organisms. In non-model species …

Motivation Thousands of genomes are publicly available, however, most genes in those
genomes have poorly defined functions. This is partly due to a gap between previously …

Automated annotations of protein functions are error-prone because of our lack of
knowledge of protein functions. For example, it is often impossible to predict the correct …

Protein structures play an important role in bioinformatics, such as in predicting gene
function or validating gene model annotation. However, determining protein structure was …

The BAHD acyltransferase family is one of the largest enzyme families in flowering plants,
containing dozens to hundreds of genes in individual genomes. Highly prevalent in …

The availability of large databases of biological sequences presents an opportunity for in-
depth exploration of gene diversity and function. Bacterial defense systems are a rich source …