SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures.

Structural Classification of Proteins-extended (SCOPe, http://scop.berkeley.edu) is a database of protein structural relationships that extends the SCOP database. SCOP is a manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. Development of the SCOP 1.x series concluded with SCOP 1.75. The ASTRAL compendium provides several databases and tools to aid in the analysis of the protein structures classified in SCOP, particularly through the use of their sequences. SCOPe extends version 1.75 of the SCOP database, using automated curation methods to classify many structures released since SCOP 1.75. We have rigorously benchmarked our automated methods to ensure that they are as accurate as manual curation, though there are many proteins to which our methods cannot be applied. SCOPe is also partially manually curated to correct some errors in SCOP. SCOPe aims to be backward compatible with SCOP, providing the same parseable files and a history of changes between all stable SCOP and SCOPe releases. SCOPe also incorporates and updates the ASTRAL database. The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank (PDB) entries, increasing the number of structures classified in SCOP by 55% and including more than 65% of the protein structures in the PDB

The kanarra fold-thrust system -- The leading edge of the sevier fold-thrust belt, southwest Utah

“The Jurassic to Eocene Sevier fold-thrust belt is the subject of continued scientific curiosity in tectonics, stratigraphy, and industry. Understanding its development in southwest Utah is hindered in part due to the multiple origins proposed for the Kanarra anticline, a major leading edge structure -- a drag fold along the Hurricane fault, Laramide monocline, Sevier fault propagation fold, or a combination of these -- which have confused its tectonic significance and regional context. This confusion results from the structural complexity of its exposed eastern limb, as well as displacement and burial of its crest and western limb beneath Neogene sediments and volcanics along the Hurricane fault. New, detailed bedrock geologic mapping of the central portion of the fold near Kanarraville, Utah and geologic cross sections restored to Cretaceous time (i.e., pre-Basin and Range extension) demonstrate the formation of a composite anticline- syncline pair and fold accommodation thrust faulting are linked in the development of this Sevier structure. A previously unrecognized thrust, the Red Rock Trail thrust, formed due to fold tightening as a “break thrust” in a favorable position to link with the basal detachment. The traditional “Kanarra anticline” is more appropriately termed the “Kanarra fold-thrust system” considering the formation of the Red Rock Trail thrust and other thrusts on the fold. The east verging Red Rock Trail thrust locally presents as a distinctive cataclasite zone in the Navajo Sandstone, which is thrust over the Jurassic Carmel and younger Cretaceous strata. Traceable from Kanarraville to Parowan Gap, this thrust is the leading edge of the Sevier fold-thrust belt in southwest Utah. Stratigraphic relationships constrain the development of the Kanarra fold-thrust system to the Late Cretaceous to Early Eocene (~80 to 50 Ma). Thus the Red Rock Trail thrust records eastward advancement of the Sevier deformation front from the Iron Springs thrust (~100 Ma, coinciding with magmatic flare-ups in the Cordilleran arc and indicating close correspondence between arc-related processes and foreland deformation”--Abstract, page iv

Deformation processes at the leading edge of the sevier fold and thrust belt, southwest Utah

Deformation processes leading to formation and abandonment of \u27triangle zones\u27 along the leading edge of the Sevier fold and thrust belt are investigated near Kanarraville, Utah through construction of a detailed geologic map and cross-section along Spring Creek. Here the eastern limb of the Kanarra fold, a Sevier structure, is well exposed along the Hurricane Cliffs due to uplift and erosion of the footwall of the Hurricane Fault. The east-verging Kanarra fold changes from upright to overturned within Spring Creek. Within the fold limb, parasitic folds, minor thrust faults, and duplex structures result in local tectonic overthickening of units and demonstrate overall east-directed tectonic transport. Results from construction of the geologic cross-section indicate the Kanarra fold is a fault propagation fold forming above a blind thrust ramp - the \u27Kanarra thrust\u27. In addition, the Taylor Creek thrust system, a system of west-directed thrust faults (backthrusts) as previously mapped along strike to the south, is inferred to be folded and overturned within the line of section. A combination of east-directed fault-related folding, the presence of a west-directed major backthrust, and the beginnings of tectonic overthickening, represent basic structural elements of a nascent \u27triangle zone\u27. This triangle zone appears to have been abandoned prior to becoming fully developed. Merging of the Kanarra thrust and the folded Taylor Creek backthrust creates an effective west-dipping ramp that circumvented development of the triangle zone by enabling the Kanarra thrust to continue to cut up section through the Navajo Sandstone (Jn). These results suggest triangle zones may be less likely to fully develop in association with fault-propagation folds in comparison to fault bend folds --Abstract, page iii

Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implications

BACKGROUND: Determining the complete repertoire of protein structures for all soluble, globular proteins in a single organism has been one of the major goals of several structural genomics projects in recent years. RESULTS: We report that this goal has nearly been reached for several "minimal organisms" – parasites or symbionts with reduced genomes – for which over 95% of the soluble, globular proteins may now be assigned folds, overall 3-D backbone structures. We analyze the structures of these proteins as they relate to cellular functions, and compare conservation of fold usage between functional categories. We also compare patterns in the conservation of folds among minimal organisms and those observed between minimal organisms and other bacteria. CONCLUSION: We find that proteins performing essential cellular functions closely related to transcription and translation exhibit a higher degree of conservation in fold usage than proteins in other functional categories. Folds related to transcription and translation functional categories were also overrepresented in minimal organisms compared to other bacteria

The Kanarra fold-thrust structure - the leading edge of the Sevier fold-thrust belt, southwestern Utah: Geology of the Intermountain West

The multiple origins proposed for the Kanarra anticline in southwestern Utah as a drag-fold along the Hurricane fault, a Laramide monocline, a Sevier fault-propagation fold, or a combination of these process­es, serve to muddy its tectonic significance. This in part reflects the structural complexity of the exposed eastern half of the fold. The fold evolved from open and up-right to overturned and tight, is cross-cut by multiple faults, and was subsequently dismembered by the Hurricane fault. The western half of the fold is obscured because of burial, along with the hanging wall of the Hurricane fault, beneath Neogene and younger sediments and volcanics. We present the results of detailed bedrock geologic mapping, and geo­logic cross sections restored to Late Cretaceous time (prior to Basin and Range extension), to demonstrate the Kanarra anticline is a compound anticline-syncline pair inextricably linked with concomitant thrust faulting that formed during the Sevier orogeny. We propose the name Kanarra fold-thrust structure to unambiguously identify the close spatial and temporal association of folding and thrusting in formation of this prominent geologic feature. We identify a previously unrecognized thrust, the Red Rock Trail thrust, as a forelimb shear thrust that was in a favorable orientation and position to have been soft-linked, and lo­cally hard-linked, with the thrust ramp of the basal detachment to form a break thrust. The east verging Red Rock Trail thrust is recognized by a distinctive cataclasite in the Lower Jurassic Navajo Sandstone. The hanging wall of the Red Rock Trail thrust is displaced eastward over the Middle Jurassic Carmel For­mation and Upper Cretaceous Formations and can be traced for at least 27 km and possibly farther. We contend the Kanarra fold-thrust structure unambiguously defines the leading edge of the Sevier fold-thrust belt in southwestern Utah. Stratigraphic relationships in the southern and northern part of the Kanarra fold-thrust structure constrain its development between the early and late Campanian (about 84 to 71 Ma) but possibly younger. In southwest Utah, initial movement along the Iron Springs thrust at about 100 Ma (Quick and others, 2020) and subsequent eastward advancement of the Sevier deformation front to the Red Rock Trail thrust at about 84 to 71 Ma coincided with well-documented magmatic flare ups in the Cordilleran arc in the hinterland of the Sevier fold-thrust belt. This temporal relationship between mag­matic flare ups and thrusting is consistent with a close correspondence between arc-related processes and episodic foreland deformation

Data growth and its impact on the SCOP database: new developments

The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. The SCOP hierarchy comprises the following levels: Species, Protein, Family, Superfamily, Fold and Class. While keeping the original classification scheme intact, we have changed the production of SCOP in order to cope with a rapid growth of new structural data and to facilitate the discovery of new protein relationships. We describe ongoing developments and new features implemented in SCOP. A new update protocol supports batch classification of new protein structures by their detected relationships at Family and Superfamily levels in contrast to our previous sequential handling of new structural data by release date. We introduce pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships. We also discuss the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop

Comparative mapping of sequence-based and structure-based protein domains

BACKGROUND: Protein domains have long been an ill-defined concept in biology. They are generally described as autonomous folding units with evolutionary and functional independence. Both structure-based and sequence-based domain definitions have been widely used. But whether these types of models alone can capture all essential features of domains is still an open question. METHODS: Here we provide insight on domain definitions through comparative mapping of two domain classification databases, one sequence-based (Pfam) and the other structure-based (SCOP). A mapping score is defined to indicate the significance of the mapping, and the properties of the mapping matrices are studied. RESULTS: The mapping results show a general agreement between the two databases, as well as many interesting areas of disagreement. In the cases of disagreement, the functional and evolutionary characteristics of the domains are examined to determine which domain definition is biologically more informative

WIST: toolkit for rapid, customized LIMS development

Summary: Workflow Information Storage Toolkit (WIST) is a set of application programming interfaces and web applications that allow for the rapid development of customized laboratory information management systems (LIMS). WIST provides common LIMS input components, and allows them to be arranged and configured using a flexible language that specifies each component's visual and semantic characteristics. WIST includes a complete set of web applications for adding, editing and viewing data, as well as a powerful setup tool that can build new LIMS modules by analyzing existing database schema