Search results for "Bioinformatic"
showing 10 items of 1651 documents
Docking and multivariate methods to explore HIV-1 drug-resistance: a comparative analysis
2007
In this paper we describe a comparative analysis between multivariate and docking methods in the study of the drug resistance to the reverse transcriptase and the protease inhibitors. In our early papers we developed a simple but efficient method to evaluate the features of compounds that are less likely to trigger resistance or are effective against mutant HIV strains, using the multivariate statistical procedures PCA and DA. In the attempt to create a more solid background for the prediction of susceptibility or resistance, we carried out a comparative analysis between our previous multivariate approach and molecular docking study. The intent of this paper is not only to find further supp…
Homology models of melatonin receptors: challenges and recent advances
2013
Melatonin exerts many of its actions through the activation of two G protein-coupled receptors (GPCRs), named MT1 and MT2. So far, a number of different MT1 and MT2 receptor homology models, built either from the prototypic structure of rhodopsin or from recently solved X-ray structures of druggable GPCRs, have been proposed. These receptor models differ in the binding modes hypothesized for melatonin and melatonergic ligands, with distinct patterns of ligand-receptor interactions and putative bioactive conformations of ligands. The receptor models will be described, and they will be discussed in light of the available information from mutagenesis experiments and ligand-based pharmacophore …
Latest advances in molecular topology applications for drug discovery
2015
Molecular topology (MT) has emerged in recent years as a powerful approach for the in silico generation of new drugs. In the last decade, its application has become more and more popular among the leading research groups in the field of quantitative structure-activity relationships (QSAR) and drug design. This has, in turn, contributed to the rapid development of new techniques and applications of MT in QSAR studies, as well as the introduction of new topological indices.This review collates the main innovative techniques in the field of MT and provides a description of the novel topological indices recently introduced, through an exhaustive recompilation of the most significant works carri…
String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins.
2011
The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, …
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
The frequency of non-syndromic distomolar teeth in a Greek population sample?
2015
Background: To investigate the frequency of non-syndromic distomolars in a Greek population sample. Material and Methods: The study population of this retrospective study consisted of 859 Orthopantomograms (OPGs) of 425 male and 434 female patients, attended the Department of Oral Diagnosis and Radiology, Dental School of Athens seeking for treatment. The OPGs were taken as a part of the patients treatment planning. Patients’ mean age was 33.57 years. Exclusion criteria from this study was cleft lip ± palate and diseases associated with systemic conditions and syndromes (such as cleidocranial dysplasia and Gardner syndrome). OPGs were only included in the study if at least one 3 rd molar wa…
Information entropy-based classification of triterpenoids and steroids from Ganoderma
2015
Abstract A set of 71 triterpenoid and steroid compounds from Ganoderma were periodically classified using a procedure based on information entropy with artificial intelligence. Six features were used in hierarchical order to classify the triterpenoids and steroids structurally. The phytochemicals belonging to the same group in the periodic table present similar antioxidant activity, and those compounds belonging to the same period exhibit maximum resemblance. The periodic classification is related to the experimental bioactivity and antioxidant potency data that are available in the literature: a steroid with a three-ketone group conjugated with two carbon–carbon double bonds in the right s…
2-exo,5-endo,8,8,10-Pentachlorobornane
2008
The title compound, C(10)H(13)Cl(5), is a polychlorinated monoterpene and a Toxaphene congener. This compound is also the only penta-chlorinated derivative of camphene formed via ionic chlorination. Previously, the title compound was thought to be 2-exo,5-endo,9,9,10-penta-chloro-bornane, but X-ray structural analysis showed it to have a different structure and rather to be 2-exo,5-endo,8,8,10-penta-chloro-bornane. The title compound shows static disorder and almost half the molecule was divided in two partitions with an occupancy ratio of 0.575 (major) to 0.425 (minor). The repulsive close contacts of Cl atoms could possibly be the cause for this disorder.
Adverse Reactions to Anticancer Drugs in the Oral Cavity
2018
The development, testing, and adoption into clinical practice of anticancer medications have revolutionized cancer care over the past decades. A better understanding of the biology of cancer has translated into development of novel systemic agents, as well a more effective use of older chemotherapy agents. As a consequence, cancer mortality continues to decrease. However, greater cure and disease control rates come at a price of an increased risk of adverse effects, which often affects the mouth and related structures including the oral mucosa, salivary glands, jawbones, and cranial nerves. Oral mucositis, hyposalivation, dysgeusia, and osteonecrosis of the jaw (ONJ) are some examples of th…
Principle considerations for the use of transcriptomics in doping research
2011
Over the course of the past decade, technical progress has enabled scientists to investigate genome-wide RNA ex- pression using microarray platforms. This transcriptomic approach represents a promising tool for the discovery of basic gene expression patterns and for identification of cellular signalling pathways under various conditions. Since doping substances have been shown to influence mRNA expression, it has been suggested that these changes can be detected by screening the blood transcriptome. In this review, we critically discuss the potential but also the pitfalls of this application as a tool in doping research. Transcriptomic approaches were considered to potentially provide resea…