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Protein Docking is an important task in computational chemistry and computational biology and yet is very computationally expensive. This paper presents a study on implementing molecular docking program in the Hadoop-based system. The molecular docking platform based on Hadoop provides the preprocessing of ligand datasets and the analysis function of the docking results, it also implements the parallel...
Molecular docking is a time consuming process, and it requires a substantial amount of computing power. D3DOCkxb was developed for investigating the effects of halogen bond in drug discovery by adding two precise score functions to Auto Dock. The docking accuracy of D3DOCkxb is better than Auto Dock, which can be attributed to a more complicated processing logic of D3DOCkxb. Consequently, it is an...
Metallothioneins (MT) are a group of low-molecular weight, cysteine rich intracellular proteins, which are encoded by a family of genes containing at least 10 functional isoforms in human. This includes MT-I, MT-II, MT-III and MT-IV. The expression and induction of these proteins have been associated with protection against DNA damage, oxidative stress and apoptosis. A number of studies have shown...
Traditional virtual screening in the grid needs chemists to upload small molecule files and collect the results manually, which cannot implement docking and collection of results automatically. This caused heavy workload to chemists. In this paper, we took advantage of Hadoop platform in the massive data storage. We stored and managed small molecule files and docking results files using HDFS. In addition,...
Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements, the world might find cures for incurable diseases like HIV disease and Cancer sooner. Our approach presented in this paper is to utilize a multi-core environment...
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...
Molecular docking technology is an important tool in computer-aided drug discovery and structure prediction for the protein-ligand complex. In this work, based on the analysis of the algorithm of the widely used the docking program AutoDock, we proposed a hybrid parallel method using the message passing interface (MPI) library. The modified programs were applied to dock the small molecule XK263 to...
Molecular docking is one of the most important methods in computer assisted drug design, with the dreg activity of flexible ligands verified during docking to macromolecular targets, its use value could be determined. Because of the large quantity of ligands in data bank, it will be extraordinarily time-consuming to compute the interaction between ligands and macromolecules. The paper lays emphasis...
The prediction of the binding affinity of protein- ligand complexes is important for the molecular docking and rational drug discovery. In this study, we have analyzed the descriptors, which affect the binding affinities of protein-ligand complexes, from five dimensions, including protein-ligand interactions, protein properties, structural and physicochemical descriptors of ligands, metal-ligand bonding,...
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