… protein search and design (1–3). However, forming a global picture of the protein universe
… In other words, a global picture needs to portray the relationships among all proteins, yet we …

… Previous work (6) suggests that the protein universe is growing rapidly and without bounds;
we find that only the MDA sequences are growing linearly with added sequences. The new …

… of thousands of known protein shapes, to identify new types of protein architecture, and to
… billions of years, between protein molecules. Protein shape comparison also improves tools …

… Here, we focus on classifications that aim at providing a global view of the protein universe.
Notice that protein databases that organize known proteins can also be interpreted as …

… In contrast, the protein shape space of the current work shows a very different view of the
protein universe. Proteins with similar protein folds (ie main-chain conformations) are placed …

… protein family. Levitt [32 •• ] provided a detailed classification of the domains in the entire
protein universe, … More recent approaches identify homologous sequences by global alignment …

… aimed at developing acomprehensive view of the protein structural universe. Structural
genomicspromises to yield a large number of experimental protein structures (tens ofthousands) …

… in the size of the protein universe expected to have occurred during evolution. … global
evolutionary relationships at a genomic scale. However, they conflict with the accepted view of a …

… nature of protein universe. We show the protein universe can be realized as a protein space
… Our protein space is constructed based on the global sequence information of proteins, and …

… appears to suggest that the protein universe is made up of a relatively … protein families.
Thus, the vast uncharacterized part of protein universe, called by some “the dark matter of protein …