A lattice model of protein conformation and dynamics is used to explore the requirements for the de novo folding from an arbitrary random coil state of idealized models of four and six-member b-barrels. A number of possible conjectures for the factors giving rise to the structural uniqueness of globular proteins are examined. These include the relative role of generic hydrophilic/ hydrophobic a...

Currently, there are a number of motif detection tools available that possess unique functionality. These tools often report different motifs, and therefore use of multiple tools is generally advised since common motifs reported by multiple tools are more likely to be biologically significant. However, results produced by these different tools need to be compared and existing similarity detecti...

Design patterns offer design motifs, solutions to object-oriented design problems. Design motifs lead to well-structured designs and thus are believed to ease software maintenance. However, after use, they are often “lost” and are consequently of little help during program comprehension and other maintenance activities. Therefore, several works proposed design pattern identification approaches ...

Noncanonical RNA motifs help define the vast complexity of RNA structure and function, and in many cases, these loops and junctions are on the order of only ten nucleotides in size. Unfortunately, despite their small size, there is no reliable method to determine the ensemble of lowest energy structures of junctions and loops at atomic accuracy. This chapter outlines straightforward protocols u...

Viroids are noncoding RNAs that infect plants. In order to establish systemic infection, these RNAs must traffic from an initially infected host cell into neighboring cells and ultimately throughout a whole plant. Recent studies have identified structural motifs in a viroid that are required for trafficking, enabling further studies on the mechanisms of their function. Some cellular proteins in...

escherichia coli (e. coli) bacteria can damage dna of the gut lining cells and may encourage the development of colon cancer according to recent reports. genetic switches are specific sequence motifs and many of them are drug targets. it is interesting to know motifs and their location in sequences. at the present study, gibbs sampler algorithm was used in order to predict and find functional m...