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The problem of the discovery and marketing of new drugs can be vastly accelerated through High Performance Computing (HPC), molecular modeling techniques, and more specifically by means of the techniques commonly named as computational drug discovery (CDD) and in silico high throughput screening. These techniques usually assume a unique interaction site (active site) between potential drugs and a...
Computer-aided drug design techniques are important assets in pharmaceutical industry because of their support for research and development of new drugs. Molecular docking (MD) predicts specific compound's binding modes within the active site of target proteins. Since MD is a time-consuming process, existing approaches reduce the number of receptors or ligands in docking by evaluating only small sets...
The application of an in-house developed web server called ChemBioServer to the filtering and selection of drug candidates for the inhibition of the PI3Kα protein is presented. 1000 candidate molecules were initially selected from a virtual screening experiment. Those molecules were then filtered for steric clashes, physicochemical and toxicity properties and grouped into clusters using the ChemBioServer...
The evolution of drug resistance in malaria continues to be a widespread concern. Many of these drugs target key proteins such as dihydrofolate reductase (DHFR). However in malaria, the structural plasticity of DHFR allows it to maintain its active site and catalytic activity, while resisting drug binding. One way to better understand this process is through the appreciation of DHFR structural evolution...
One of the major challenges in systems biology today is to devise robust methods of interpreting data concerning the expression levels of the genes in an organism in a way that will shed light on the collective interactions between multiple genes and their products. The ability to better understand and predict the structures and actions of complex biological systems is of significant importance to...
Following the availability of whole genome sequence of Mycobacterium tuberculosis (MTB) in public database, the anticipation of its benefits would definitely falls into the contribution towards development of improved vaccine or drug discovery to fight against the fatal disease, tuberculosis (TB). This research aimed to scan the whole genome sequence of MTB by application of bioinformatics approaches...
Despite intense investment growth and technology development, there is an observed bottleneck in drug discovery and development over the past decade. NIH started the Molecular Libraries Initiative (MLI) in 2004 to enlarge the pool for potential drug targets, especially from the “undruggable” part of human genome, and potential drug candidates from much broader types of drug-like small molecules. In...
Core regulatory modules play fundamental roles in amassing, processing and dispatching genetic information during whole cell life cycle. Currently most clustering methods fail to abstract inherent biological contents from related high-throughput expression profiles, although they may reduce high dimension to a certain low one. The work proposes a weighted structural model clustering method for integrative...
WISDOM is an international initiative to deploy large-scale in-silico docking on a public grid infrastructure in an attempt to find potential drugs against neglected or emerging diseases such as Malaria and Avian Flu. Within the framework of the WISDOM initiative, large-scale deployments of in silico docking have been done on production grid infrastructures, demonstrating the relevance of large scale...
In this paper, a new algorithm related with feature selection method mostly used in data mining, machine learning and pattern recognition areas is proposed. Classical Fukunaga-Koontz Transform is extended to a binary kernel classifier. We used cDNA microarrays to assess 11.000 gene expression profiles in 60 human cancer cell lines used in a drug discovery screen by the National Cancer Institute and...
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...
MAPK cell signal transduction pathways determine the survival of the cells. If one can control this pathways, and then they will prohibit the proliferation of the cancer cells. Furthermore, they will heal the cancer smoothly. In order to attain this goal, we use lots of drugs to interact with MEK1 in MAPK, by using computer aided drug design to analyze the ligand activity of proteins in MEK1.
Semantic Capability Description Language (SCDL) plays an important role as a common language and provides a generic format for problem formalization. In this paper we extend SCDL to include typical applications in drug discovery and development that include similarity and substructure searches, quantitative structure activity relationship modeling and in silico docking experiments.
The following topics are dealt with: bioinformatics; biomedical imaging; biomedical image analysis; biomaterials; gene expression analysis; gene identification; gene classification; protein structure prediction; molecular simulation; systems biology; bio-sets; biomedical data engineering; drug discovery; molecular evolution; semantic biomedical computing and phylogeny.
Culturing cells in a vascularized three-dimensional (3D) hydrogel scaffold has significant applications ranging from tissue engineering to drug discovery. In many large 3D scaffolds, mass transport and nutrient exchange leads to cell necrosis, limiting functionality. Here we present a technique for fabricating microfluidic channels in cell-laden methacrylated hyaluronic acid (MeHA) hydrogels. Using...
DrugScreener-G is an integrated environment for virtual screening with grid computing. It implements basic ideas of grid-enabled large-scale virtual screening into a concrete software suite, especially emphasizing user friendliness and accessibility to grid computing. DrugScreener-G aims at providing users without knowledge of grid computing with an intuitive and easy-to-use integrated environment...
High performance computing has become a major focus of attention by government, industry, medical centers and academic institutions. The U.S. government has made this a ldquotop national priorityrdquo, linking the development of a ldquodata superhighway systemrdquo to national competitiveness and national research interest. High performance supercomputing approaches have been used for sequence analysis,...
Increasingly drug discovery is turning to in-silico methods to find potential enzyme or protein-protein inhibitors. The quantitative structure-activity relationship (QSAR) is commonly used to find potential inhibitors in the search for new drugs. In this paper we propose to use a radial basis function (RBF) network to determine the QSAR of aldose reductase inhibitors (ARIs). We find that the RBF network...
A Petri net was used to model, analyze, and ultimately control a novel laboratory robotic system designed to automatically image protein crystallization experiments per user-specified schedules. Flexibility in system operation was necessary in order to accommodate unpredictable experimental tray entry and removal by crystallographers, as well as on-the-fly modification of imaging schedules to account...
About 40% of all marketed drugs have the so-called G-protein coupled receptors (GPCRs) as their target protein. There exist more than 800 different GPCRs in humans, of which at least 300 GPCRs are believed to be druggable. Yet, for only two GPCRs there are three-dimensional (3D) protein crystal structures available and consequently little is known about the molecular interactions between pharmacologically...
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