Abstract:
:Motif3D is a web-based protein structure viewer designed to allow sequence motifs, and in particular those contained in the fingerprints of the PRINTS database, to be visualised on three-dimensional (3D) structures. Additional functionality is provided for the rhodopsin-like G protein-coupled receptors, enabling fingerprint motifs of any of the receptors in this family to be mapped onto the single structure available, that of bovine rhodopsin. Motif3D can be used via the web interface available at: http://www.bioinf.man.ac.uk/dbbrowser/motif3d/motif3d.html.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gaulton A,Attwood TKdoi
10.1093/nar/gkg534keywords:
subject
Has Abstractpub_date
2003-07-01 00:00:00pages
3333-6issue
13eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw958
更新日期:2017-01-25 00:00:00
abstract::Mouse DNA contains two equally abundant, homologous subfamilies of MspI 3.6 and 5 kb repeated fragments. The first subfamily corresponds to the previously described (1) Bam 4 kb repeats, the second one to Bam repeated fragments of higher molecular weight. These subfamilies account for the vast majority of long Bam rep...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.3.1593
更新日期:1984-02-10 00:00:00
abstract::Alternative splicing is widespread in mammalian gene expression, and variant splice patterns are often specific to different stages of development, particular tissues or a disease state. There is a need to systematically collect data on alternatively spliced exons, introns and splice isoforms, and to annotate this dat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh030
更新日期:2004-01-01 00:00:00
abstract::Phenotype analysis is commonly recognized to be of great importance for gaining insight into genetic interaction underlying inherited diseases. However, few computational contributions have been proposed for this purpose, mainly owing to lack of controlled clinical information easily accessible and structured for comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki454
更新日期:2005-07-01 00:00:00
abstract::Apolipoprotein B (apoB) mRNA editing is a nuclear event that minimally requires the RNA substrate, APOBEC-1 and APOBEC-1 Complementation Factor (ACF). The co-localization of these macro-molecules within the nucleus and the modulation of hepatic apoB mRNA editing activity have been described following a variety of meta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl417
更新日期:2006-07-04 00:00:00
abstract::Complementary DNA clones encoding the human kidney epidermal growth factor (EGF) precursor have been isolated and sequenced. They predict the sequence of a 1,207 amino acid protein which contains EGF flanked by polypeptide segments of 970 and 184 residues at its NH2- and COOH-termini, respectively. The structural orga...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.21.8427
更新日期:1986-11-11 00:00:00
abstract::Unwanted side effects of drugs are a burden on patients and a severe impediment in the development of new drugs. At the same time, adverse drug reactions (ADRs) recorded during clinical trials are an important source of human phenotypic data. It is therefore essential to combine data on drugs, targets and side effects...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1075
更新日期:2016-01-04 00:00:00
abstract::Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10-20% repeated DNA sequences. There are...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.11.1411
更新日期:1974-11-01 00:00:00
abstract::The proportion of cytosines methylated in the DNA of nucleosome oligomers and of core particles appears indistinguishable from that of total nuclear DNA from CHO cells. However the DNA in nucleoprotein which is initially released from nuclei by treatment with very low levels of micrococcal nuclease and the first 10% o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.9.3097
更新日期:1977-09-01 00:00:00
abstract::mRNA expression involves transcription initiation, elongation and degradation. In cells, these dynamic processes are highly regulated. However, experimental characterization of the dynamic processes in vivo is difficult due to the paucity of methods capable of direct measurements. We present a highly sensitive and ver...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw596
更新日期:2016-10-14 00:00:00
abstract::TcruziDB (http://TcruziDB.org) is an integrated genome database for the parasitic organism Trypanosoma cruzi, the causative agent of Chagas' disease. The database currently incorporates all available sequence data (Genomic, BAC, EST) in a single user-friendly location. The database contains a variety of tools specific...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh049
更新日期:2004-01-01 00:00:00
abstract::Quantitative real-time PCR has revolutionized many aspects of genetic research, biomedical diagnostics and pathogen detection. Nevertheless, the full potential of this technology has yet to be realized, primarily due to the limitations of the threshold-based methodologies that are currently used for quantitative analy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh177
更新日期:2004-12-15 00:00:00
abstract::Error-free lesion bypass and error-prone lesion bypass are important cellular responses to DNA damage during replication, both of which require a DNA polymerase (Pol). To identify lesion bypass DNA polymerases, we have purified human Polkappa encoded by the DINB1 gene and examined its response to damaged DNA templates...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.21.4138
更新日期:2000-11-01 00:00:00
abstract::Given that greater than 90% of the human genome is expressed, it is logical to assume that post-transcriptional regulatory mechanisms must be the primary means of controlling the flow of information from mRNA to protein. This report describes a robust approach that includes in silico, in vitro and in cellulo experimen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq557
更新日期:2010-11-01 00:00:00
abstract::The higher order structure of the functionally important 530 loop in Escherichia coli 16S rRNA was studied in mutants with single base changes at position 517, which significantly impair translational fidelity. The 530 loop has been proposed to interact with the EF-Tu-GTP-aatRNA ternary complex during decoding. The re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.17.3563
更新日期:1995-09-11 00:00:00
abstract::A complete physical map of the spinach mitochondrial genome has been established. The entire sequence content of 327 kilobase pairs (kb) is postulated to occur as a single circular molecule. Two directly repeated elements of approximately 6 kb, located on this "master chromosome", are proposed to participate in an int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.14.5651
更新日期:1986-07-25 00:00:00
abstract::The products of the RAG-1 and RAG-2 genes are essential for the recombination of the DNA encoding the antigen receptors of the developing immune system. Little is known of the specific role these genes play. We have explored the sequences encoding mouse RAG-1 by deleting large parts of the gene and by introducing loca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.24.5644
更新日期:1993-12-11 00:00:00
abstract::MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally val...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn707
更新日期:2009-01-01 00:00:00
abstract::MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz757
更新日期:2020-01-08 00:00:00
abstract::DNA binding of heat shock factor 2 (HSF2) is induced during hemin-induced differentiation of human erythroleukemia cell line K562. To identify the transcriptional activation and the regulatory domains of HSF2, we constructed a series of deletion derivatives fused to the yeast GAL4 DNA binding domain and analyzed their...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2580
更新日期:1998-06-01 00:00:00
abstract::Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5'-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr467
更新日期:2011-07-01 00:00:00
abstract::A method for quantifying the proportion of supercoiled circular (SC) forms in DNA solutions is described. The method (SCFluo) takes advantage of the reversible denaturation property of SC forms and the high specificity of the PicoGreen fluorochrome for double-stranded (ds)DNA. Fluorescence values of forms capable of r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.12.e57
更新日期:2000-06-15 00:00:00
abstract::Brome mosaic virus (BMV) is a tripartite genome, positive-sense RNA virus of plants. Previously it was demonstrated that local hybridization between BMV RNAs (RNA-RNA heteroduplex formation) efficiently promotes non-homologous RNA recombination. In addition, studies on the role of the BMV polymerase in RNA recombinati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.8.1714
更新日期:2000-04-15 00:00:00
abstract::The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt808
更新日期:2013-12-01 00:00:00
abstract::A growing body of evidence suggests that siRNA could generate off-target effects through different mechanisms. However, the full impact of off-target gene regulation on phenotypic induction and accordingly on data interpretation in the context of large-scale siRNA library screen has not been reported. Here we report o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki762
更新日期:2005-08-09 00:00:00
abstract::The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm176
更新日期:2007-01-01 00:00:00
abstract::The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subuni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky618
更新日期:2018-09-06 00:00:00
abstract::KpnI restriction of DNAs from all anthropoid primates studied releases a conspicuous series of segments representing families of long, interspersed repetitive DNAs termed here the KpnI 1.2, 1.5, 1.8 and 1.9 kb families. Human KpnI 1.2 to 1.9 kb segments representative of these families were isolated and separately clo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.10.3175
更新日期:1982-05-25 00:00:00
abstract::ATP-dependent type I topoisomerases from extremely thermophilic archaebacteria--reverse gyrases--drive positive supercoiling of DNA. We showed that reverse gyrase from Desulfurococcus amylolyticus breaks the DNA at specific sites and covalently binds to the 5' end. In 30 out of 31 sites located in pBR322 DNA fragments...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.9.2801
更新日期:1990-05-11 00:00:00
abstract::An enzyme activity introducing an alkali-labile site at 2-hydroxyadenine (2-OH-A) in double-stranded oligonucleotides was detected in nuclear extracts of Jurkat cells. This activity co-eluted with activities toward adenine paired with guanine and 8-oxo-7,8-dihydroguanine (8-oxoG) as a single peak corresponding to a 55...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.6.1355
更新日期:2000-03-15 00:00:00