Saccharomyces cerevisiae is one of the best-studied model organisms, yet the three-dimensional structure and molecular function of many yeast proteins remain unknown. Yeast proteins were parsed into 14,934 domains, and those lacking sequence similarity to proteins of known structure were folded using the Rosetta de novo structure prediction method on the World Community Grid. This structural da...

The Fragnostic (http://ffas.burnham.org/Fragnostic) web tool implements a novel and useful view of protein structure space. We mined a non-redundant subset of the PDB for common fragments shared between proteins inhabiting different SCOP folds. Subsequently, we formulated an inter-fold similarity measure based on fragment sharing. Fold space is described as a graph whose nodes are folds between...

The database of multiple alignments for protein structures (DMAPS) provides instant access to pre-computed multiple structure alignments for all protein structure families in the Protein Data Bank (PDB). Protein structure families have been obtained from four distinct classification methods including SCOP, CATH, ENZYME and CE, and multiple structure alignments have been built for all families c...

Finding similarity between a pair of protein structures is one of the fundamental tasks in many areas of bioinformatical research such as protein structure prediction, function mapping, etc. We propose a method for finding pairing of amino acids based on densities of the structures and we also propose a modification to the original template modeling-score (TM-Score) rotation algorithm that asse...

The Structural Classi®cation of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known protein structures. The classi®cation is on hierarchical levels: the ®rst two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relat...

The quantum inspired State Context Property (SCOP) theory of concepts is unique amongst theories of concepts in offering a means of incorporating that for each concept in each different context there are an unlimited number of exemplars, or states, of varying degrees of typicality. Working with data from a study in which participants were asked to rate the typicality of exemplars of a concept f...

OBJECTIVES Effects of acute exposure to organophosphorous pesticides (OPs), chlorphenvinphos (CVP) or chlorphyriphos (CPF) on amphetamine (AMPH)- or scopolamine (SCOP)-induced open-field locomotion were compared in rats. MATERIALS AND METHODS CVP and CPF were administered intraperitoneally, both at doses resulting in about 50% inhibition of erythrocyte acetylcholinesterase (rbcAChE). The pest...

The development of automatic approaches for the comparison of protein sequences has become increasingly important. Methods that compare profiles allow for the use of information about whole protein families, resulting in more sensitive and accurate detection of distantly related sequences. In this contribution, we describe a thorough optimization and tests of a profile-to-profile alignment meth...

Sanguisorba officinalis L. is known to have anti-inflammatory properties. However, the potential effects of S. officinalis against asthma have not been reported. In the present study, we investigated the protective effects and underlying mechanisms of S. officinalis in a murine ovalbumin (OVA)-induced asthma model. Mice were sensitized and challenged by OVA inhalation to induce airway inflammat...