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N. Perdigão, J. Heinrich, C. Stolte, K. S. Sabir, M. J. Buckley, B. Tabor, B. Signal, B. S. Gloss, C. J. Hammang, B. Rost, A. Schafferhans, S. I. O'Donoghue (Instituto Superior Técnico - Universidade de Lisboa; Commonwealth Scientific and Industrial Research Organisation (CSIRO); Garvan Institute of Medical Research; Technische Universität München)We surveyed the “dark” proteome – that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44 – 54% of the proteome in eukaryotes and viruses was dark, compared with only ∼ 14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.