Abstract:
:SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at http://supfam.org/. Hidden Markov models based on Structural Classification of Proteins (SCOP) domain definitions at the superfamily level are used to provide structural annotation. We recently produced a new model library based on SCOP 1.73. Family level assignments are also available. From the web site users can submit sequences for SCOP domain classification; search for keywords such as superfamilies, families, organism names, models and sequence identifiers; find over- and underrepresented families or superfamilies within a genome relative to other genomes or groups of genomes; compare domain architectures across selections of genomes and finally build multiple sequence alignments between Protein Data Bank (PDB), genomic and custom sequences. Recent extensions to the database include InterPro abstracts and Gene Ontology terms for superfamiles, taxonomic visualization of the distribution of families across the tree of life, searches for functionally similar domain architectures and phylogenetic trees. The database, models and associated scripts are available for download from the ftp site.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wilson D,Pethica R,Zhou Y,Talbot C,Vogel C,Madera M,Chothia C,Gough Jdoi
10.1093/nar/gkn762subject
Has Abstractpub_date
2009-01-01 00:00:00pages
D380-6issue
Database issueeissn
0305-1048issn
1362-4962pii
gkn762journal_volume
37pub_type
杂志文章abstract::We have carried out a survey of potential quadruplex structure sequences (PQSS), which occur in the immediate upstream region (500 bp) of human genes. By examining the number and distribution of these we have established that there is a clear link between them and the occurrence of the SP1-binding element 'GGGCGG', su...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn078
更新日期:2008-05-01 00:00:00
abstract::The delivery of site-specific post-translational modifications to histones generates an epigenetic regulatory network that directs fundamental DNA-mediated processes and governs key stages in development. Methylation of histone H4 lysine-20 has been implicated in DNA repair, transcriptional silencing, genomic stabilit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt776
更新日期:2014-01-01 00:00:00
abstract::Protein-RNA interactions in small nuclear ribonucleoproteins (UsnRNPs) from HeLa cells were investigated by irradiation of purified nucleoplasmic snRNPs U1 to U6 with UV light at 254 nm. The cross-linked proteins were analyzed on one- and two-dimensional gel electrophoresis systems, and the existence of a stable cross...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.23.10985
更新日期:1988-12-09 00:00:00
abstract::The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1070
更新日期:2018-01-04 00:00:00
abstract::TP63, a member of the p53 gene family gene, encodes the ΔNp63 protein and is one of the most frequently amplified genes in squamous cell carcinomas (SCC) of the head and neck (HNSCC) and lungs (LUSC). Using an epiallelic series of siRNAs with intrinsically different knockdown abilities, we show that the complete loss ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw036
更新日期:2016-04-20 00:00:00
abstract::DAXX displays complex biological functions. Remarkably, DAXX overexpression is a common feature in diverse cancers, which correlates with tumorigenesis, disease progression and treatment resistance. Structurally, DAXX is modular with an N-terminal helical bundle, a docking site for many DAXX interactors (e.g. p53 and ...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkz634
更新日期:2019-09-05 00:00:00
abstract::Trf4/5p-Air1/2p-Mtr4p polyadenylation complex (TRAMP) is an essential component of nuclear RNA surveillance in yeast. It recognizes a variety of nuclear transcripts produced by all three RNA polymerases, adds short poly(A) tails to aberrant or unstable RNAs and activates the exosome for their degradation. Despite the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks223
更新日期:2012-07-01 00:00:00
abstract::The DNA damage response is vigorously activated by DNA double-strand breaks (DSBs). The chief mobilizer of the DSB response is the ATM protein kinase. We discovered that the COP9 signalosome (CSN) is a crucial player in the DSB response and an ATM target. CSN is a protein complex that regulates the activity of cullin ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv270
更新日期:2015-05-19 00:00:00
abstract::Unmodified tRNA molecules are useful for many purposes in cell-free protein biosynthesis, but there is little information about how the lack of tRNA post-transcriptional modifications affects the coding specificity for synonymous codons. In the present study, we prepared an unmodified form of Escherichia coli tRNA1Ser...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.15.2894
更新日期:1996-08-01 00:00:00
abstract::Telomere G-quadruplex is emerging as a promising anti-cancer target due to its inhibition to telomerase, an enzyme expressed in more than 85% tumors. Telomerase-mediated telomere extension and some other reactions require a free 3' telomere end in single-stranded form. G-quadruplex formation near the 3' end of telomer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr164
更新日期:2011-08-01 00:00:00
abstract::Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh.uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp431
更新日期:2009-07-01 00:00:00
abstract::Nematode mitochondria expresses two types of extremely truncated tRNAs that are specifically recognized by two distinct elongation factor Tu (EF-Tu) species named EF-Tu1 and EF-Tu2. This is unlike the canonical EF-Tu molecule that participates in the standard protein biosynthesis systems, which basically recognizes al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki784
更新日期:2005-08-19 00:00:00
abstract::We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky019
更新日期:2018-04-20 00:00:00
abstract::The locus control region is required for high-level, position-independent expression of mammalian beta-globin genes. It is marked by five major DNase hypersensitive sites (HSs) in a 16 kb region of chromatin, and the protein-DNA complexes that form these HSs may interact in a holocomplex that carries out the full func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.21.4327
更新日期:1996-11-01 00:00:00
abstract::We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distributio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz905
更新日期:2019-12-02 00:00:00
abstract::We report here the different ways in which four subunits of the basal transcription/repair factor TFIIH (XPB, XPD, p62 and p44) and the damage recognition XPC repair protein can enter the nucleus. We examined their nuclear localization by transiently expressing the gene products tagged with the enhanced green fluoresc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.7.1574
更新日期:2001-04-01 00:00:00
abstract::The mitochondrial DNA (mtDNA) control regions for common chimpanzee, pygmy chimpanzee and gorilla were sequenced and the lengths and termini of their D-loop DNA's characterized. In these and all other species for which there are data, 5' termini map to sequences that contain the trinucleotide YAY. 3' termini are 25-51...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.13.5841
更新日期:1988-07-11 00:00:00
abstract::A synapomorphy is a phylogenetic character that provides evidence of shared descent. Ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. With the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl440
更新日期:2006-01-01 00:00:00
abstract::Circular DNA aptamers are powerful candidates for therapeutic applications given their dramatically enhanced biostability. Herein we report the first effort to evolve circular DNA aptamers that bind a human protein directly in serum, a complex biofluid. Targeting human thrombin, this strategy has led to the discovery ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa800
更新日期:2020-11-04 00:00:00
abstract::Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buff...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx553
更新日期:2017-09-06 00:00:00
abstract::BRCA1 expression is repressed by aberrant cytosine methylation in sporadic breast cancer. We hypothesized that aberrant cytosine methylation of the BRCA1 promoter was associated with the transcriptionally repressive effects of histone hypoacetylation and chromatin condensation. To address this question, we developed a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.17.3233
更新日期:2000-09-01 00:00:00
abstract::We examined the influence of the tetratricopeptide repeat factor XAB2 on chromosomal break repair, and found that XAB2 promotes end resection that generates the 3' ssDNA intermediate for homologous recombination (HR). Namely, XAB2 is important for chromosomal double-strand break (DSB) repair via two pathways of HR tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw275
更新日期:2016-07-08 00:00:00
abstract::Investigation of biological processes using selective chemical interventions is generally applied in biomedical research and drug discovery. Many studies of this kind make use of gene expression experiments to explore cellular responses to chemical interventions. Recently, some research groups constructed libraries of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn610
更新日期:2008-11-01 00:00:00
abstract::A single base change in 16S rRNA (C726 to G) has previously been shown to have a dramatic effect on protein synthesis in E. coli (1). This paper more specifically details the effects of the mutation on mRNA binding and translation-termination. The in vitro technique of toeprinting (2) was used to demonstrate that 30S ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.18.5381
更新日期:1990-09-25 00:00:00
abstract::CCG repeats are highly over-represented in exons of the human genome. Usually they are located in the 5' UTR but are also abundant in translated sequences. The CCG repeats are associated with three tri-nucleotide repeat disorders: Huntington's disease, myotonic dystrophy type 1 and chromosome X-linked mental retardati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks557
更新日期:2012-09-01 00:00:00
abstract::Human somatic cells have essentially no telomerase activity. Telomerase is linked to tumor genesis and is a valuable marker for malignant growth. Extreme paucity of the enzyme neccessitated development of a PCR-based assay, 'telomeric repeat amplification protocol' (TRAP). Unfortunately, this method is not without dif...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.4.919
更新日期:1997-02-15 00:00:00
abstract::Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv563
更新日期:2015-10-15 00:00:00
abstract::In two-colour microarrays, the ratio of signal intensities of two co-hybridized samples is used as a relative measure of gene expression. Ratio-based analysis becomes complicated and inefficient in multi-class comparisons. We therefore investigated the validity of an intensity-based analysis procedure. To this end, tw...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh038
更新日期:2004-02-24 00:00:00
abstract::DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.21.4303
更新日期:1995-11-11 00:00:00
abstract::Long-range enhancers of transcription are a key component of the genomic regulatory architecture. Recent studies have identified bi-directionally transcribed RNAs emanating from these enhancers known as eRNAs. However, it remains unclear how tightly coupled eRNA production is with enhancer activity. Through our system...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1018
更新日期:2014-11-10 00:00:00