We investigate 25-34 nucleotide RNA sequences, that have been rationally designed to adopt two different secondary structures that are in thermodynamic equilibrium. Experimental evidence for the co-existence of the two conformers results from the NH...N 1H NMR spectra. When compared to the NH...N 1H NMR spectra of appropriate reference sequences the equilibrium position is easily quantifiable e...

A wealth of interesting computational problems arises in proposed methods for discovering new pharmaceuticals. This paper surveys our recent work in three key areas, using a Physical Geometric Algorithm (PGA) approach to data interpretation, experiment planning, and drug design: (1) Data-directed computational protocols for highthroughput protein structure determination. A key component of stru...

High-throughput functional protein NMR studies, like protein interactions or dynamics, require an automated approach for the assignment of the protein backbone. With the availability of a growing number of protein 3D structures, a new class of automated approaches, called structure-based assignment, has been developed quite recently. Structure-based approaches use primarily NMR input data that ...

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...

Actinomycetes are inexhaustible producers of commercially valuable metabolites, are continually screened for beneficial compounds. The taxonomic and phylogenetic study of novel actinomycetes strains are mostly based on conventional methods and primary DNA structure of 16s rRNA. Although 16s rRNA sequence is well accepted in phylogeny studies, its secondary structures have not been widely used. ...

Recent studies suggest that reducing the induction temperature would improve the quality of some recombinant inclusion bodies (IB) by providing a native-like secondary structure and leading to an improvement in protein recovery. This study focused on optimizing the solubilization condition of Reteplase, a recombinant protein with 9 disulfide bonds. The influence of lowering induction temperatur...