RNABase is a unified database of all three-dimensional structures containing RNA deposited in either the Protein Data Bank (PDB) or Nucleic Acid Data Base (NDB). For each structure, RNABase contains a brief summary as well as annotation of conformational parameters, identification of possible model errors, Ramachandran-style conformational maps and classification of ribonucleotides into conform...

Previous research with both brain-damaged and neurologically intact populations has demonstrated that the right cerebral hemisphere (RH) is superior to the left cerebral hemisphere (LH) at detecting anomalies (or incongruities) in objects (Ramachandran, 1995; Smith, Tays, Dixon, & Bulman-Fleming, 2002). The current research assesses whether the RH advantage for anomaly detection is due to the R...

The dynamics of surfactin, a lipopeptide surfactant from Bacillus subtilis, has been studied by molecular dynamics at different interfacial concentrations in a water-hexane medium reproducing a hydrophilic/hydrophobic biphasic system. The shapes and orientations of surfactin molecules, as hydrogen bonds and Ramachandran angles, have been recorded to investigate the environment effect on the mol...

RNA interference (RNAi) is a post-transcriptional process initiated by double-stranded RNA molecules that degrade a complementary target RNA. In the first step, long double-stranded RNA molecules are chopped into shorter duplexes by an endonuclease dubbed DICER. This work focused on the identification of phosphorylation sites in DICER and proceeded towards comparative modeling. The domain of un...

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In this paper we present a novel method to describe the pose (position and orientation) distribution of amino acid residue pairs within a protein, which are proximal in space and distal in sequence.While the Ramachandran plot provides information of protein conformations using the φ and ψ angles between sequentially proximal residues, our method can offer six-dimensional relative pose informati...

The aim of this study was to develop a theoretical model using Anopheles gambiae GSTE2 structure as template for Aedes aegypti GSTE2 by homology modeling Docking simulations were performed for both the enzymes against usnic acid in neutral and anionic forms. Ramachandran plot revealed that 93.9% of the GSTE2 model residues were located on most favored regions. Model evaluation was made by the A...

We demonstrate a calculated alpha-helix peptide folding energy landscape which accurately simulates the first experimentally measured alpha-helix melting energy landscape. We examine a 21-amino acid, mainly polyalanine peptide and calculate the free energy along the Psi Ramachandran angle secondary folding coordinate. The experimental free energy landscape was determined using UV resonance Rama...

T HE supraglottic airways have gained firm places in anesthetic practice since clinical introduction of the laryngeal mask airway (LMA) Classic (LMA North America, Inc., San Diego, CA) in 1988. Although they are generally being used safely, serious complications occasionally do occur during the use of the airways. To increase safety, we need to know the types, severity, and possible causative f...