GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studi...

Abstract Viroids are smallest, single-stranded, circular, highly structured plant pathogenic RNAs that do not code for any protein. Viroids belong to two families, the Avsunviroidae and the Pospiviroidae. Members of the Pospiviroidae family adopt a rod-like secondary structure. In this study the most stable secondary structures of citrus viroid variants that reported from Fars province wer...

Two-dimensional 1H NMR spectroscopy is used to examine the structure and mobility of cytochrome b5 in solution. The assignment of many residues and the interpretation of nuclear Overhauser effects (NOEs) in both redox states allow definition of secondary structural elements. Comparison with X-ray diffraction data shows that differences between crystal and solution structures are small. The dyna...

MOTIVATION Most secondary structure prediction programs target only alpha helix and beta sheet structures and summarize all other structures in the random coil pseudo class. However, such an assignment often ignores existing local ordering in so-called random coil regions. Signatures for such ordering are distinct dihedral angle pattern. For this reason, we propose as an alternative approach to...

Recent studies questioned whether the Protein Data Bank (PDB) contains all compact, single domain protein structures. Here, we show that all quasi-spherical, QS, random protein structures devoid of secondary structure are in the PDB and are excellent templates for all native PDB proteins up to 250 residues. Because QS templates have a similar global contour as native, TASSER can refine 98% (90%...

This paper develops a multiple channel assignment model, which allows to take advantage of spectrum opportunities in cognitive radio networks in the most efficient way. The developed scheme allows making several assignments of available and frequency adjacent channel, which require a bigger bandwidth, under an equality environment. The hybrid assignment model it is made by two algorithms, one t...

background: rna plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. rna secondary structure represents various significant portions of rna tertiary structure. since the biological function of rna is concluded indirectly from its primary structure, it would be important to analyze the relations between the rna sequences and t...

We introduce the “Automated Structure-based Assignment” problem: Given a reference 3D structure, a protein sequence, and its NMR spectra, automatically interpret the NMR spectra and do backbone resonance assignment. We then propose a solution to solve this problem. The core of the solution is a novel integer linear programming model, which is a general framework for many versions of the structu...