Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in comb...

The wealth of available protein structural data provides unprecedented opportunity to study and better understand the underlying principles of protein folding and protein structure evolution. A key to achieving this lies in the ability to analyse these data and to organize them in a coherent classification scheme. Over the past years several protein classifications have been developed that aim ...

In this work, three types of natural clays including kaolinite, montmorillonite, and illite with different molecular structures, as adsorbents, are selected for the removal of methylene blue dye, and their performance is investigated. Also the optimization and the analysis of the dye adsorption mechanism are performed using the response surface methodology, molecular modeling, and experimental ...