共查询到20条相似文献,搜索用时 31 毫秒
1.
Background
It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical methods for finding domains in sequences of amino acids. 相似文献2.
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data 总被引:1,自引:0,他引:1
Bin Chen Xiao Dong Dazhi Jiao Huijun Wang Qian Zhu Ying Ding David J Wild 《BMC bioinformatics》2010,11(1):255
Background
Recently there has been an explosion of new data sources about genes, proteins, genetic variations, chemical compounds, diseases and drugs. Integration of these data sources and the identification of patterns that go across them is of critical interest. Initiatives such as Bio2RDF and LODD have tackled the problem of linking biological data and drug data respectively using RDF. Thus far, the inclusion of chemogenomic and systems chemical biology information that crosses the domains of chemistry and biology has been very limited 相似文献3.
Background
A number of recent papers have cast doubt on the applicability of the quasispecies concept to virus evolution, and have argued that population genetics is a more appropriate framework to describe virus evolution than quasispecies theory. 相似文献4.
Ian Walsh Alberto JM Martin Catherine Mooney Enrico Rubagotti Alessandro Vullo Gianluca Pollastri 《BMC bioinformatics》2009,10(1):195-19
Background
Proteins, especially larger ones, are often composed of individual evolutionary units, domains, which have their own function and structural fold. Predicting domains is an important intermediate step in protein analyses, including the prediction of protein structures. 相似文献5.
Background
Classical bioconjugation strategies for generating antibody-functionalized nanoparticles are non-specific and typically result in heterogeneous compounds that can be compromised in activity. Expression systems based on self-cleavable intein domains allow the generation of recombinant proteins with a C-terminal thioester, providing a unique handle for site-specific conjugation using native chemical ligation (NCL). However, current methods to generate antibody fragments with C-terminal thioesters require cumbersome refolding procedures, effectively preventing application of NCL for antibody-mediated targeting and molecular imaging. 相似文献6.
Background
Extracellular domains of the Notch family of signalling receptors contain many EGF repeat domains, as do their major ligands. Some EGF repeats are modified by O-fucosylation, and most have no identified role in ligand binding. 相似文献7.
Background
FYVE domains have emerged as membrane-targeting domains highly specific for phosphatidylinositol 3-phosphate (PtdIns(3)P). They are predominantly found in proteins involved in various trafficking pathways. Although FYVE domains may function as individual modules, dimers or in partnership with other proteins, structurally, all FYVE domains share a fold comprising two small characteristic double-stranded β-sheets, and a C-terminal α-helix, which houses eight conserved Zn2+ ion-binding cysteines. To date, the structural, biochemical, and biophysical mechanisms for subcellular targeting of FYVE domains for proteins from various model organisms have been worked out but plant FYVE domains remain noticeably under-investigated. 相似文献8.
Background
Proteins of the tetraspanin family contain four transmembrane domains (TM1-4) linked by two extracellular loops and a short intracellular loop, and have short intracellular N- and C-termini. While structure and function analysis of the larger extracellular loop has been performed, the organization and role of transmembrane domains have not been systematically assessed. 相似文献9.
Background
Protein domains have long been an ill-defined concept in biology. They are generally described as autonomous folding units with evolutionary and functional independence. Both structure-based and sequence-based domain definitions have been widely used. But whether these types of models alone can capture all essential features of domains is still an open question. 相似文献10.
Background
Numerous microarray analysis programs have been created through the efforts of Open Source software development projects. Providing browser-based interfaces that allow these programs to be executed over the Internet enhances the applicability and utility of these analytic software tools. 相似文献11.
Pekka Marttinen Adam Baldwin William P Hanage Chris Dowson Eshwar Mahenthiralingam Jukka Corander 《BMC bioinformatics》2008,9(1):421
Background
We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases. 相似文献12.
Background
Cyclic nucleotides are ubiquitous intracellular messengers. Until recently, the roles of cyclic nucleotides in plant cells have proven difficult to uncover. With an understanding of the protein domains which can bind cyclic nucleotides (CNB and GAF domains) we scanned the completed genomes of the higher plants Arabidopsis thaliana (mustard weed) and Oryza sativa (rice) for the effectors of these signalling molecules. 相似文献13.
Tuula Klaavuniemi Nanna Alho Pirta Hotulainen Annina Kelloniemi Heli Havukainen Perttu Permi Sampo Mattila Jari Ylänne 《BMC cell biology》2009,10(1):22-13
Background
The PDZ-LIM proteins are a family of signalling adaptors that interact with the actin cross-linking protein, α-actinin, via their PDZ domains or via internal regions between the PDZ and LIM domains. Three of the PDZ-LIM proteins have a conserved 26-residue ZM motif in the internal region, but the structure of the internal region is unknown. 相似文献14.
Nodin Weddington Alexander Stuy Ichiro Hiratani Tyrone Ryba Tomoki Yokochi David M Gilbert 《BMC bioinformatics》2008,9(1):530
Background
Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property of specific cell types. 相似文献15.
Background
Spidroins are a unique family of large, structural proteins that make up the bulk of spider silk fibers. Due to the highly variable nature of their repetitive sequences, spidroin evolutionary relationships have principally been determined from their non-repetitive carboxy (C)-terminal domains, though they offer limited character data. The few known spidroin amino (N)-terminal domains have been difficult to obtain, but potentially contain critical phylogenetic information for reconstructing the diversification of spider silks. Here we used silk gland expression data (ESTs) from highly divergent species to evaluate the functional significance and phylogenetic utility of spidroin N-terminal domains. 相似文献16.
Background
The identification of protein domains plays an important role in protein structure comparison. Domain query size and composition are critical to structure similarity search algorithms such as the Vector Alignment Search Tool (VAST), the method employed for computing related protein structures in NCBI Entrez system. Currently, domains identified on the basis of structural compactness are used for VAST computations. In this study, we have investigated how alternative definitions of domains derived from conserved sequence alignments in the Conserved Domain Database (CDD) would affect the domain comparisons and structure similarity search performance of VAST. 相似文献17.
Background
Given the costs of signalling, why do males often advertise their fighting ability to rivals using several signals rather than just one? Multiple signalling theories have developed largely in studies of sexual signals, and less is known about their applicability to intra-sexual communication. We here investigate the evolutionary basis for the intricate agonistic signalling system in eland antelopes, paying particular attention to the evolutionary phenomenon of loud knee-clicking. 相似文献18.
Tinatin I. Brelidze Anne E. Carlson Douglas R. Davies Lance J. Stewart William N. Zagotta 《PloS one》2010,5(9)
Background
Ether-à-go-go (EAG) channels are expressed throughout the central nervous system and are also crucial regulators of cell cycle and tumor progression. The large intracellular amino- and carboxy- terminal domains of EAG1 each share similarity with known ligand binding motifs in other proteins, yet EAG1 channels have no known regulatory ligands.Methodology/Principal Findings
Here we screened a library of small biologically relevant molecules against EAG1 channels with a novel two-pronged screen to identify channel regulators. In one arm of the screen we used electrophysiology to assess the functional effects of the library compounds on full-length EAG1 channels. In an orthogonal arm, we used tryptophan fluorescence to screen for binding of the library compounds to the isolated C-terminal region.Conclusions/Significance
Several compounds from the flavonoid, indole and benzofuran chemical families emerged as binding partners and/or regulators of EAG1 channels. The two-prong screen can aid ligand and drug discovery for ligand-binding domains of other ion channels. 相似文献19.
Jun Wu Qingchao Qiu Lu Xie Joseph Fullerton Jian Yu Yu Shyr Alfred L George Yajun Yi 《BMC bioinformatics》2009,10(1):420
Background
Widespread use of high-throughput techniques such as microarrays to monitor gene expression levels has resulted in an explosive growth of data sets in public domains. Integration and exploration of these complex and heterogeneous data have become a major challenge. 相似文献20.