共查询到20条相似文献,搜索用时 15 毫秒
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Realistic simulation of biological networks requires stochastic simulation approaches because of the small numbers of molecules per cell. The high computational cost of stochastic simulation on conventional microprocessor-based computers arises from the intrinsic disparity between the sequential steps executed by a microprocessor program and the highly parallel nature of information flow within biochemical networks. This disparity is reduced with the Field Programmable Gate Array (FPGA)-based approach presented here. The parallel architecture of FPGAs, which can simulate the basic reaction steps of biological networks, attains simulation rates at least an order of magnitude greater than currently available microprocessors. 相似文献
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van Haagen HH 't Hoen PA de Morrée A van Roon-Mom WM Peters DJ Roos M Mons B van Ommen GJ Schuemie MJ 《Proteomics》2011,11(5):843-853
We introduce a framework for predicting novel protein-protein interactions (PPIs), based on Fisher's method for combining probabilities of predictions that are based on different data sources, such as the biomedical literature, protein domain and mRNA expression information. Our method compares favorably to our previous method based on text-mining alone and other methods such as STRING. We evaluated our algorithms through the prediction of experimentally found protein interactions underlying Muscular Dystrophy, Huntington's Disease and Polycystic Kidney Disease, which had not yet been recorded in protein-protein interaction databases. We found a 1.74-fold increase in the mean average prediction precision for dysferlin and a 3.09-fold for huntingtin when compared to STRING. The top 10 of predicted interaction partners of huntingtin were analysed in depth. Five were identified previously, and the other five were new potential interaction partners. The full matrix of human protein pairs and their prediction scores are available for download. Our framework can be extended to predict other types of relationships such as proteins in a complex, pathway or related disease mechanisms. 相似文献
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Thomas M. Ehrman David J. Barlow Peter J. Hylands 《Bioorganic & medicinal chemistry》2010,18(6):2204-2218
Chinese herbs were screened for compounds which may be active against four targets involved in inflammation, using pharmacophore-assisted docking. Multiple LigandScout (LS) pharmacophores built from ligand–receptor complexes in the protein databank (PDB) were first employed to select compounds. These compounds were then docked using LS-derived templates and ranked according to docking score. The targets comprised cyclo-oxygenases 1 & 2 (COX), p38 MAP kinase (p38), c-Jun terminal-NH2 kinase (JNK) and type 4 cAMP-specific phosphodiesterase (PDE4). The results revealed that multi-target inhibitors are likely to be relatively common in Chinese herbs. Details of their distribution are given, in addition to experimental evidence supporting these results. Examples of compounds predicted to be active against at least three targets are presented, and their features outlined. The distribution of herbs containing predicted inhibitors was also analysed in relation to 192 Chinese formulas from over 50 herbal categories. Among those found to contain a high proportion of these herbs were formulas traditionally used to treat fever, headache, rheumatoid arthritis, inflammatory bowel disorders, skin disease, cancer, and traumatic injury. Relationships between multi-target drug discovery and Chinese medicine are discussed. 相似文献
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Twenty-two potential miRNAs from seven miRNA families were first predicted from more than 80,857 EST sequences of peach (Prunus persica). Using two specific 5′ and 3′ miRNA RACE (miR-RACE) PCR reactions and sequence-directed cloning, we accurately determined
the precise sequences, especially both ends, of eight candidate miRNAs. The sequencing results demonstrated that the ppe-miRNAs
were conserved to those that were predicted computationally except ppe-miR171b. We validated the existence of two members
(ppe-miR171a and miR171b) of the miR171 family in peach that belonged to different precursors. qRT-PCR was further employed
in analyzing expression of the eight miRNAs in peach leaves, flowers, and fruits at different developing stages, where some
of the miRNAs showed tissue-specific expression. 相似文献
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Arnaud Lehner Laurence Menu-Bouaouiche Flavien Dardelle Fran?ois Le Mauff Azeddine Driouich Patrice Lerouge Jean-Claude Mollet 《Plant signaling & behavior》2015,10(6)
Two independent studies have shown that the cell wall of pollen tubes from tobacco and tomato species contained fucosylated xyloglucan (XyG). These findings are intriguing as many reports have shown that XyG of somatic cells of these species is not fucosylated but instead is arabinosylated. In order to produce fucosylated XyG, plants must express a functional galactoside α-2-fucosyltransferase. Here, using a bioinformatics approach, we show that several candidate genes coding for XyG fucosyltransferases are present in the genome of coffee and several Solanaceae species including tomato, tobacco, potato, eggplant and pepper. BLAST and protein alignments with the 2 well-characterized XyG fucosyltransferases from Arabidopsis thaliana and Pisum sativum revealed that at least 6 proteins from different Solanaceae species and from coffee displayed the 3 conserved motifs required for XyG fucosyltransferase activity. 相似文献
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Tyler Alioto Konstantinos G. Alexiou Amlie Bardil Fabio Barteri Raúl Castanera Fernando Cruz Amit Dhingra Henri Duval ngel Fernndez i Martí Leonor Frias Beatriz Galn Jos L. García Werner Howad Jssica Gmez‐Garrido Marta Gut Irene Julca Jordi Morata Pere Puigdomnech Paolo Ribeca María J. Rubio Cabetas Anna Vlasova Michelle Wirthensohn Jordi Garcia‐Mas Toni Gabaldn Josep M. Casacuberta Pere Arús 《The Plant journal : for cell and molecular biology》2020,101(2):455-472
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A genome-scale metabolic model of the Gram-positive bacteria Corynebacterium glutamicum ATCC 13032 was constructed comprising 446 reactions and 411 metabolites, based on the annotated genome and available biochemical information. The network was analyzed using constraint based methods. The model was extensively validated against published flux data, and flux distribution values were found to correlate well between simulations and experiments. The split pathway of the lysine synthesis pathway of C. glutamicum was investigated, and it was found that the direct dehydrogenase variant gave a higher lysine yield than the alternative succinyl pathway at high lysine production rates. The NADPH demand of the network was not found to be critical for lysine production until lysine yields exceeded 55% (mmol lysine (mmol glucose)(-1)). The model was validated during growth on the organic acids acetate and lactate. Comparable flux values between in silico model and experimental values were seen, although some differences in the phenotypic behavior between the model and the experimental data were observed. 相似文献
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Michell O. Almeida Gustavo H. G. Trossini Vinícius G. Maltarollo Danielle da C. Silva 《Journal of biomolecular structure & dynamics》2016,34(9):2045-2053
Studies have showed that there are many biological targets related to the cancer treatment, for example, TGF type I receptor (TGF-βRI or ALK5). The ALK5 inhibition is a strategy to treat some types of cancer, such as breast, lung, and pancreas. Here, we performed CoMFA and CoMSIA studies for 70 ligands with ALK5 inhibition. The internal validation for both models (q2LOO = 0.887 and 0.822, respectively) showed their robustness, while the external validations showed their predictive power (CoMFA: r2test = 0.998; CoMSIA: r2test = 0.975). After all validations, CoMFA and CoMSIA maps indicated physicochemical evidences on the main factors involved in the interaction between bioactive ligands and ALK5. Therefore, these results suggest molecular modifications to design new ALK5 inhibitors. 相似文献
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Ramos-Echazábal G Chinea G García-Fernández R Pons T 《Journal of cellular biochemistry》2012,113(7):2364-2374
Human nucleophosmin/B23 is a phosphoprotein involved in ribosome biogenesis, centrosome duplication, cancer, and apoptosis. Its function, localization, and mobility within cells, are highly regulated by phosphorylation events. Up to 21 phosphosites of B23 have been experimentally verified even though the corresponding kinase is known only for seven of them. In this work, we predict the phosphorylation sites in human B23 using six kinase-specific servers (KinasePhos 2.0, PredPhospho, NetPhosK 1.0, PKC Scan, pkaPS, and MetaPredPS) plus DISPHOS 1.3, which is not kinase specific. The results were integrated with information regarding 3D structure and residue conservation of B23, as well as cellular localizations, cellular processes, signaling pathways and protein-protein interaction networks involving both B23 and each predicted kinase. Thus, all 40 potential phosphosites of B23 were predicted with significant score (>0.50) as substrates of at least one of 38 kinases. Thirteen of these residues are newly proposed showing high susceptibility of phosphorylation considering their solvent accessibility. Our results also suggest that the enzymes CDKs, PKC, CK2, PLK1, and PKA could phosphorylate B23 at higher number of sites than those previously reported. Furthermore, PDK, GSK3, ATM, MAPK, PKB, and CHK1 could mediate multisite phosphorylation of B23, although they have not been verified as kinases for this protein. Finally, we suggest that B23 phosphorylation is related to cellular processes such as apoptosis, cell survival, cell proliferation, and response to DNA damage stimulus, in which these kinases are involved. These predictions could contribute to a better understanding, as well as addressing further experimental studies, of B23 phosphorylation. 相似文献
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In plasma membranes, lipids distribute asymmetrically across the bilayer, a process that requires proteins. Recent work identified novel lipid translocators in yeast, and their activity was functionally correlated to endocytosis, thus boosting investigations on identity, mechanism, and function of lipid translocases. 相似文献
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M. Rubio P. Martínez‐Gómez J. A. García F. Dicenta 《The Annals of applied biology》2013,163(3):466-474
Grafting almond variety ‘Garrigues’ onto ‘GF305’ peach seedlings heavily infected by Plum pox virus (PPV) progressively produces the disappearance of viral symptoms and drastically reduces virus accumulation in ‘GF305’ rootstock, in most cases to undetectable levels. This response appears to be specific between almond and peach, as it was not consistently observed by grafting ‘Garrigues’ onto other Prunus species such as plum (‘Adesoto’) or apricot (‘Real Fino’). The ability to induce resistance to PPV in ‘GF305’ was transmitted to the sexual descendants of Garrigues. Furthermore, grafting ‘Garrigues’ onto ‘GF305’ before PPV inoculation completely prevented virus infection, showing that the resistance is constitutive and not induced by the virus. This fact suggests that resistance may be due to the transfer of a defence factor from ‘Garrigues’ almond through the graft union and its interaction with specific factors of ‘GF305’ peach to produce the antiviral response. These results open new avenues to potential protection against PPV in peach, the most economically important species among stone fruits. 相似文献