共查询到20条相似文献,搜索用时 15 毫秒
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Grishin NV 《Cell》2012,149(7):1424-1425
A daring experiment is performed. Using sequence alignments to predict contacts between residues in protein spatial structures, Hopf et al. are publishing untested de novo structure models for 11 transmembrane protein families. Will their models stand the test of time and hold up to experimentation? The prospects are excellent. 相似文献
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Hopkins MM Ibarreta D Gaisser S Enzing CM Ryan J Martin PA Lewis G Detmar S van den Akker-van Marle ME Hedgecoe AM Nightingale P Dreiling M Hartig KJ Vullings W Forde T 《Nature biotechnology》2006,24(4):403-410
Genetics is slowly explaining variations in drug response, but applying this knowledge depends on implementation of a host of policies that provide long-term support to the field, from translational research and regulation to professional education. 相似文献
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Background
An important class of interaction switches for biological circuits and disease pathways are short binding motifs. However, the biological experiments to find these binding motifs are often laborious and expensive. With the availability of protein interaction data, novel binding motifs can be discovered computationally: by applying standard motif extracting algorithms on protein sequence sets each interacting with either a common protein or a protein group with similar properties. The underlying assumption is that proteins with common interacting partners will share some common binding motifs. Although novel binding motifs have been discovered with such approach, it is not applicable if a protein interacts with very few other proteins or when prior knowledge of protein group is not available or erroneous. Experimental noise in input interaction data can further deteriorate the dismal performance of such approaches. 相似文献5.
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Milosavljevic A 《Nature biotechnology》2010,28(10):1053-1056
Comparative analysis of epigenomes offers new opportunities to understand cellular differentiation, mutation effects and disease processes. But the scale and heterogeneity of epigenetic data present numerous computational challenges. 相似文献
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Currently available protein-protein interaction (PPI) network or 'interactome' maps, obtained with the yeast two-hybrid (Y2H) assay or by co-affinity purification followed by mass spectrometry (co-AP/MS), only cover a fraction of the complete PPI networks. These partial networks display scale-free topologies--most proteins participate in only a few interactions whereas a few proteins have many interaction partners. Here we analyze whether the scale-free topologies of the partial networks obtained from Y2H assays can be used to accurately infer the topology of complete interactomes. We generated four theoretical interaction networks of different topologies (random, exponential, power law, truncated normal). Partial sampling of these networks resulted in sub-networks with topological characteristics that were virtually indistinguishable from those of currently available Y2H-derived partial interactome maps. We conclude that given the current limited coverage levels, the observed scale-free topology of existing interactome maps cannot be confidently extrapolated to complete interactomes. 相似文献
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The import of proteins into mitochondria occurs in several steps. At least three of these steps require ATP and involve molecular chaperones. This energy requirement has served as a useful tool for elucidating the import pathways into the four mitochondrial compartments. 相似文献
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MOTIVATION: Graph drawing algorithms are often used for visualizing relational information, but a naive implementation of a graph drawing algorithm encounters real difficulties when drawing large-scale graphs such as protein interaction networks. RESULTS: We have developed a new, extremely fast layout algorithm for visualizing large-scale protein interaction networks in the three-dimensional space. The algorithm (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of this algorithm over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases and (3) it provides several abstraction and comparison operations for effectively analyzing large-scale protein interaction networks. AVAILABILITY: http://wilab.inha.ac.kr/interviewer/ 相似文献
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Schächter V 《BioTechniques》2002,(Z1):16-8, 20-4, 26-7
We survey recent techniques for construction and prediction of large-scale protein interaction networks, focusing on computational processing steps. Special emphasis is placed on critical assessment of data completeness and reliability of the various approaches. Once built, protein interaction networks can be used for functional annotation or to generate higher-level biological hypotheses on pathways. 相似文献
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Modular organization of protein interaction networks 总被引:6,自引:0,他引:6
Luo F Yang Y Chen CF Chang R Zhou J Scheuermann RH 《Bioinformatics (Oxford, England)》2007,23(2):207-214
MOTIVATION: Accumulating evidence suggests that biological systems are composed of interacting, separable, functional modules. Identifying these modules is essential to understand the organization of biological systems. RESULT: In this paper, we present a framework to identify modules within biological networks. In this approach, the concept of degree is extended from the single vertex to the sub-graph, and a formal definition of module in a network is used. A new agglomerative algorithm was developed to identify modules from the network by combining the new module definition with the relative edge order generated by the Girvan-Newman (G-N) algorithm. A JAVA program, MoNet, was developed to implement the algorithm. Applying MoNet to the yeast core protein interaction network from the database of interacting proteins (DIP) identified 86 simple modules with sizes larger than three proteins. The modules obtained are significantly enriched in proteins with related biological process Gene Ontology terms. A comparison between the MoNet modules and modules defined by Radicchi et al. (2004) indicates that MoNet modules show stronger co-clustering of related genes and are more robust to ties in betweenness values. Further, the MoNet output retains the adjacent relationships between modules and allows the construction of an interaction web of modules providing insight regarding the relationships between different functional modules. Thus, MoNet provides an objective approach to understand the organization and interactions of biological processes in cellular systems. AVAILABILITY: MoNet is available upon request from the authors. 相似文献
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Bork P 《Bioinformatics (Oxford, England)》2002,18(Z2):S64
Recent advances in proteomics and computational biology have lead to a flood of protein interaction data and resulting interaction networks (e.g. (Gavin et al., 2002)). Here I first analyse the status and quality of parts lists (genes and proteins), then comparatively assess large-scale protein interaction data (von Mering et al., 2002) and finally try to identify biological meaningful units (e.g. pathways, cellular processes) within interaction networks that are derived from the conservation of gene neighborhood (Snel et al., 2002). Possible extensions of gene neighborhood analysis to eukaryotes (von Mering and Bork, 2002) will be discussed. 相似文献
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Luo Feng; Yang Yunfeng; Chen Chin-Fu; Chang Roger; Zhou Jizhong; Scheuermann Richard H. 《Bioinformatics (Oxford, England)》2007,23(7):916
Bioinformatics (2007) 23(2), 相似文献