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Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful...
Drugs and biological experiments are designed to affect a particular target gene or pathway. However, they might inadvertently activate other pathways and cause side effects. Because of the existence of complex cellular mechanisms responding to stimuli, it is difficult to detect the presence of such side effects. Therefore, identification of pathways that function together under identical conditions...
It has been shown previously that glucocorticoids exert a dual mechanism of action, meaning cytotoxic and mitogenic as well as mitogenic and anti-apoptotic, in a dose-dependent manner on CCRF-CEM cells at 72 h. Early gene expression response suggested also a dose-dependent dual mechanism of action of prednisolone which is apparently reflected on cell state upon 72 h of treatment. The present work...
G-protein-coupled receptors (GPCRs) share a characteristic core composed of seven-transmembrane ??-helices represent by far the largest family of cell-surface molecules involved in signal transmission, accounting for ??2% of the total genes encoded by the human genome. At present, most data types supplied by databases of GPCRs and relative proteins are mainly protein structure data, ligand binding...
Mathematical modeling gene regulatory networks is important for understanding and controlling them, with various drugs and their dosage regimens. The ordinary differential equations approach is sensible but also very difficult. Our reverse engineering algorithm (RODES), based on neural networks feedback linearization and genetic programming, takes as inputs high-throughput (e.g., microarray) time...
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle lead to important scientific advances and provide a powerful new tool for drug discovery. A wide range of biologically important processes, however, occur over time scales on the order of a millisecond ~ several orders of magnitude beyond the duration...
According to the mechanism clarification problem of traditional Chinese medicine (TCM), a systems biology platform was constructed using the related achievements as the basis, entity grammar systems as the framework and database construction, data mining, qualitative reasoning as the kernel techniques. This platform is composed of TCM active components database, TCM prescription database, drug targets...
Graph data mining algorithms are increasingly applied to biological graph dataset. However, while existing graph mining algorithms can identify frequently occurring sub-graphs, these do not necessarily represent useful patterns. In this paper, we propose a novel graph mining algorithm, MIGDAC (Mining Graph DAta for Classification), that applies graph theory and an interestingness measure to discover...
Life science industry has been flourished with the explosion of online Bioinformatics databases and tools, which can affect the drug discovery process and development. The integration of unstructured data, available in biomedical literature (i.e. PubMED), and structured data, existing in biological databases, by applying both text and data mining techniques is a very critical issue in order to identify...
Genetic algorithm in the bioinformatic can be categorised into many different groups by the implementations they were instructed. Each approach has its own pros and cons. When making a choice between GA approaches to data mining, it is important that the scientist knows the advantages and disadvantages of each approach. In this project a suitable GA strategy will be identified and refined, based on...
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