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A procedure for automated protein structure determination is presented that is based on an iterative procedure during which the NOESY peak list assignment and the structure calculation are performed simultaneously. The input consists of a list of NOESY peak positions and a list of chemical shifts as obtained from sequence-specific resonance assignment. For(More)
We explain the notion of software-defined networking (SDN), whose southbound interface may be implemented by the OpenFlow protocol. We describe the operation of OpenFlow and summarize the features of specification versions 1.0–1.4. We give an overview of existing SDN-based applications grouped by topic areas. Finally, we point out architectural design(More)
A new method for automatically assigning proton-proton NOESY spectra is described and demonstrated for simulated and experimental spectra of the proteins dendrotoxin K, alpha-amylase inhibitor tendamistat and the DNA-binding domain of the 434 repressor protein. The method assigns the NOESY spectrum and calculates three-dimensional protein structures(More)
Metallothioneins are small cysteine-rich proteins capable of binding heavy metal ions such as Zn2+ and Cd2+. They are ubiquitous tissue components in higher organisms, which tentatively have been attributed both unspecific protective functions against toxic metal ions and highly specific roles in fundamental zinc-regulated cellular processes. In this paper(More)
The NOAH/DIAMOD program suite was used to automatically assign an experimental 2D NOESY spectrum of the 46 residue protein crambin(S22/I25), using feedback filtering and self-correcting distance geometry (SECODG). Automatically picked NOESY cross peaks were combined with 157 manually assigned peaks to start NOAH/DIAMOD calculations. At each cycle, DIAMOD(More)
BACKGROUND Metastases of renal cell carcinoma (RCC) to the thyroid gland are uncommon. There is no clear consensus regarding the role of surgery in metastatic disease to the thyroid since most clinical studies include small numbers of patients. Also, risk factors associated with disease progression following thyroidectomy are not yet defined. We examined(More)
The three-dimensional structure of [Cd7]-metallothionein-2 from rat liver was determined in aqueous solution, using nuclear magnetic resonance spectrometry and distance geometry calculations. The experimental data provided proton-proton distance constraints from measurements of nuclear Overhauser effects, constraints on the geometry of the metal-cysteine(More)
In this paper we consider carrier networks using only OpenFlow switches instead of IP routers. Accommodating the full forwarding information base (FIB) of IP routers in the switches is difficult because the BGP routing tables in the default-free zone currently contain about 500,000 entries and switches have only little capacity in their fast and expensive(More)
Maximally redundant trees (MRTs) have been suggested in IETF as a new promising method for fast rerouting in IP networks. Unlike loop-free alternates (LFAs), they can protect against all link and node failures if topology allows. In this work, we compare MRTs and not-via addresses, which also guarantee full-failure coverage. We evaluate path lengths and(More)
Attractin, a 58-residue protein secreted by the mollusk Aplysia californica, stimulates sexually mature animals to approach egg cordons. Attractin from five different Aplysia species are approximately 40% identical in sequence. Recombinant attractin, expressed in insect cells and purified by reverse-phase high-performance liquid chromatography (RP-HPLC), is(More)