SAM-T08, HMM-based protein structure prediction

The SAM-T08 web server is a protein structure prediction server that provides several useful intermediate results in addition to the final predicted 3D structure: three multiple sequence alignments of putative homologs using different iterated search procedures, prediction of local structure features including various backbone and burial properties, calibrated E-values for the significance of template searches of PDB and residue–residue contact predictions. The server has been validated as part of the CASP8 assessment of structure prediction as having good performance across all classes of predictions. The SAM-T08 server is available at http://compbio.soe.ucsc.edu/SAM_T08/T08-query.htm

Walking commodities: a multi-isotopic approach (δ13C, δ15N, δ34S, 14C and 87/86Sr) to trace the animal economy of the Viking Age town of Birka

Carbon (δ13C), nitrogen (δ15N), and strontium (87/86Sr) isotope analyses have been applied widely over the past four decades to reconstruct human and animal dietary and mobility patterns. Sulfur (δ34S) has recently shown great promise to further enhance isotope analyses of the geologic and hydrologic contexts in which organic material formed. For this case study we applied this suite of multi-isotopic analyses to a dataset of 45 animal bones and teeth from the urban Viking Age town of Birka located in present-day Sweden. This research falls in line with previous studies as a potential way to bridge the understanding of relationships between centers and hinterlands by tracing socioeconomic networks of subsistence and food provisioning utilizing the animal economy as a proxy. The utilization of δ34S values enables terrestrial, marine and freshwater food niches to be disentangled when δ13C and δ15N values may be overlapping between each of the niches. The incorporation of five 87/86Sr samples further allowed us to carefully interpret the movement of animals across the landscape. We identified cattle potentially originating > 180 km from Birka during the earliest stages of occupation (early 8th century CE), while pigs and ovicaprids were more locally reared, indicating the dimensions of the early market economy in the Viking period was complex and multifaceted

The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions

The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/~genome/gtop.html) freely provides an extensive collection of information on protein structures and functions obtained by application of various computational tools to the amino acid sequences of entirely sequenced genomes. GTOP contains annotations of 3D structures, protein families, functions, and other useful data of a protein of interest in user-friendly ways to give a deep insight into the protein structure. From the initial 1999 version, GTOP has been continually updated to reap the fruits of genome projects and augmented to supply novel information, in particular intrinsically disordered regions. As intrinsically disordered regions constitute a considerable fraction of proteins and often play crucial roles especially in eukaryotes, their assignments give important additional clues to the functionality of proteins. Additionally, we have incorporated the following features into GTOP: a platform independent structural viewer, results of HMM searches against SCOP and Pfam, secondary structure predictions, color display of exon boundaries in eukaryotic proteins, assignments of gene ontology terms, search tools, and master files

Multi-Overlap Simulations for Transitions between Reference Configurations

We introduce a new procedure to construct weight factors, which flatten the probability density of the overlap with respect to some pre-defined reference configuration. This allows one to overcome free energy barriers in the overlap variable. Subsequently, we generalize the approach to deal with the overlaps with respect to two reference configurations so that transitions between them are induced. We illustrate our approach by simulations of the brainpeptide Met-enkephalin with the ECEPP/2 energy function using the global-energy-minimum and the second lowest-energy states as reference configurations. The free energy is obtained as functions of the dihedral and the root-mean-square distances from these two configurations. The latter allows one to identify the transition state and to estimate its associated free energy barrier.Comment: 12 pages, (RevTeX), 14 figures, Phys. Rev. E, submitte

Ein Beitrag zur klinischen Diagnostik des ektopischen ACTH-Syndroms

Es wird über einen Fall von ektopischem ACTH-Syndrom mit Hypercortizismus und hypokaliämischer Alkalose bei einem metastasierten Pankreas-Carcinom berichtet. Das Fehlen einer Differenz zwischen den ACTH-Spiegeln im Plasma aus dem Bulbus cranialis venae jugularis und aus der Vena femoralis unterstützte die Annahme einer nicht hypophysären Herkunft der erhöhten ACTH-Spiegel.A case of ectopic ACTH syndrome is reported presenting with hypercorticism and pronounced hypokalemic alkalosis in a woman aged 55 y. with metastatic cancer of the pancreas. The failure to show a significant difference of plasma ACTH-levels from bulbus superior venae jugularis resp. femoral vein supported the clinical assumption of non pituitary origin of elevated plasma ACTH

Islands of change vs. islands of disaster: Managing pigs and birds in the Anthropocene of the North Atlantic

The offshore islands of the North Atlantic were among some of the last settled places on earth, with humans reaching the Faroes and Iceland in the late Iron Age and Viking period. While older accounts emphasizing deforestation and soil erosion have presented this story of island colonization as yet another social–ecological disaster, recent archaeological and paleoenvironmental research combined with environmental history, environmental humanities, and bioscience is providing a more complex understanding of long-term human ecodynamics in these northern islands. An ongoing interdisciplinary investigation of the management of domestic pigs and wild bird populations in Faroes and Iceland is presented as an example of sustained resource management using local and traditional knowledge to create structures for successful wild fowl management on the millennial scale

EasyModeller: A graphical interface to MODELLER

<p>Abstract</p> <p>Background</p> <p>MODELLER is a program for automated protein Homology Modeling. It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently.</p> <p>Findings</p> <p>The study was designed with an aim to develop of "EasyModeller" tool as a frontend graphical interface to MODELLER using Perl/Tk, which can be used as a standalone tool in windows platform with MODELLER and Python preinstalled. It helps inexperienced users to perform modeling, assessment, visualization, and optimization of protein models in a simple and straightforward way.</p> <p>Conclusion</p> <p>EasyModeller provides a graphical straight forward interface and functions as a stand-alone tool which can be used in a standard personal computer with Microsoft Windows as the operating system.</p

MMDB: 3D structures and macromolecular interactions

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure

Annotated chemical patent corpus: A gold standard for text mining

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, t