Abstract:
:We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into evolutionary families and structural groupings. We currently identify 827 homologous families in which the proteins have both structual similarity and sequence and/or functional similarity. These can be further clustered into 593 fold groups and 32 distinct architectures. Using our structural classification and associated data on protein functions, stored in the database (EC identifiers, SWISS-PROT keywords and information from the Enzyme database and literature) we have been able to analyse the correlation between the 3D structure and function. More than 96% of folds in the PDB are associated with a single homologous family. However, within the superfolds, three or more different functions are observed. Considering enzyme functions, more than 95% of clearly homologous families exhibit either single or closely related functions, as demonstrated by the EC identifiers of their relatives. Our analysis supports the view that determining structures, for example as part of a 'structural genomics' initiative, will make a major contribution to interpreting genome data.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Orengo CA,Pearl FM,Bray JE,Todd AE,Martin AC,Lo Conte L,Thornton JMdoi
10.1093/nar/27.1.275subject
Has Abstractpub_date
1999-01-01 00:00:00pages
275-9issue
1eissn
0305-1048issn
1362-4962pii
gkc089journal_volume
27pub_type
杂志文章abstract::Sequencing of RNAs (RNA-Seq) has revolutionized the field of transcriptomics, but the reads obtained often contain errors. Read error correction can have a large impact on our ability to accurately assemble transcripts. This is especially true for de novo transcriptome analysis, where a reference genome is not availab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt215
更新日期:2013-05-01 00:00:00
abstract::Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated 'CasHRA (Cas9-facilitated Homologous Recombination Ass...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw475
更新日期:2016-08-19 00:00:00
abstract::Bile acid biosynthesis is subjected to feedback regulation whereby bile acids down-regulate their own synthesis. The major point of this regulation is at the level of cholesterol 7alpha-hydroxylase (7alpha-hydroxylase), which controls bile acid output from the classic pathway. This regulation is at the level of transc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.18.3587
更新日期:2000-09-15 00:00:00
abstract::Here we describe a two-stepped photobiotin-based procedure to enrich a target (canine retinal) cDNA library for tissue specific clones without removing those containing repetitive ( SINE ) elements, despite the presence of these elements in the driver population. In a first hybridization excess SINE elements were hybr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.21.4427
更新日期:1997-11-01 00:00:00
abstract::In the known monoclinic crystals the 3-dimensional structure of the hexameric, replicative helicase RepA encoded by plasmid RSF1010 shows 6-fold rotational symmetry. In contrast, in the cubic crystal form at 2.55 A resolution described here RepA has 3-fold symmetry and consists of a trimer of dimers. To study structur...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg790
更新日期:2003-10-15 00:00:00
abstract::Synthesis and radioiodination of a stannyl oligodeoxyribonucleotide were undertaken to evaluate a gamma ray emitting ODN ligand for thrombus imaging in vivo . Synthesis of the ODN was based on modified automatedbeta-cyanoethyl phosphoramidite chemistry with an organotin nucleoside (dU*) coupled to a thrombin binding a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.14.2897
更新日期:1997-07-15 00:00:00
abstract::The task of gene identification frequently confronting researchers working with both novel and well studied genomes can be conveniently and reliably solved with the help of the GeneMark web software (http://opal.biology.gatech.edu/GeneMark/). The website provides interfaces to the GeneMark family of programs designed ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki487
更新日期:2005-07-01 00:00:00
abstract::Mitochondrial DNA maintenance and segregation are dependent on the actin cytoskeleton in budding yeast. We found two cytoskeletal proteins among six proteins tightly associated with rat liver mitochondrial DNA: non-muscle myosin heavy chain IIA and β-actin. In human cells, transient gene silencing of MYH9 (encoding no...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr052
更新日期:2011-07-01 00:00:00
abstract::MicroRNAs are a class of small non-coding RNAs that serve as important regulators of gene expression at the posttranscriptional level. They are stable in body fluids and pose great potential to serve as biomarkers. Here, we present a highly specific, sensitive and cost-effective system to quantify miRNA expression bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx588
更新日期:2017-09-06 00:00:00
abstract::Leishmania species are protozoan parasites whose remarkably plastic genome limits the establishment of effective genetic manipulation and leishmaniasis treatment. The strategies used by Leishmania to maintain its genome while allowing variability are not fully understood. Here, we used DiCre-mediated conditional gene ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1017
更新日期:2018-12-14 00:00:00
abstract::Increasing numbers of proteins, nucleic acids and other molecular entities have been explored as therapeutic targets, hundreds of which are targets of approved and clinical trial drugs. Knowledge of these targets and corresponding drugs, particularly those in clinical uses and trials, is highly useful for facilitating...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1014
更新日期:2010-01-01 00:00:00
abstract::The gene encoding the DNA methyltransferase M.CviRI from Chlorella virus XZ-6E was cloned and expressed in Escherichia coli. M.CviRI methylates adenine in TGCA sequences. DNA containing the M.CviRI gene was sequenced and a single open reading frame of 1137 bp was identified which could code for a polypeptide of 379 am...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.2.307
更新日期:1991-01-25 00:00:00
abstract::Expression of a proof-reading deficient form of mitochondrial DNA (mtDNA) polymerase gamma, POLG, causes early death accompanied by features of premature ageing in mouse. However, the mechanism of cellular senescence remains unresolved. In addition to high levels of point mutations of mtDNA, the POLG mutator mouse har...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp091
更新日期:2009-04-01 00:00:00
abstract::p73, the p53 homologue, exists as a transactivation-domain-proficient TAp73 or deficient deltaN(DN)p73 form. Expectedly, the oncogenic DNp73 that is capable of inactivating both TAp73 and p53 function, is over-expressed in cancers. However, the role of TAp73, which exhibits tumour-suppressive properties in gain or los...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn414
更新日期:2008-08-01 00:00:00
abstract::Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1245
更新日期:2019-02-20 00:00:00
abstract::We previously found that the splicing of exon 5 to exon 6 in the rat beta-TM gene required that exon 6 first be joined to the downstream common exon 8 (Helfman et al., Genes and Dev. 2, 1627-1638, 1988). Pre-mRNAs containing exon 5, intron 5 and exon 6 are not normally spliced in vitro. We have carried out a mutationa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.12.2318
更新日期:1994-06-25 00:00:00
abstract::CS23D (chemical shift to 3D structure) is a web server for rapidly generating accurate 3D protein structures using only assigned nuclear magnetic resonance (NMR) chemical shifts and sequence data as input. Unlike conventional NMR methods, CS23D requires no NOE and/or J-coupling data to perform its calculations. CS23D ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn305
更新日期:2008-07-01 00:00:00
abstract::Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa898
更新日期:2021-01-08 00:00:00
abstract::The RDM1 gene encodes a RNA recognition motif (RRM)-containing protein involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. We previously reported a cDNA encoding the full-length human RDM1 protein. Here, we describe the identification of 11 human cDNAs encoding RDM1 protein isoforms. Th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm753
更新日期:2007-01-01 00:00:00
abstract::The transcriptional silencing of one of the female X-chromosomes is a finely regulated process that requires accumulation in cis of the long non-coding RNA X-inactive-specific transcript (Xist) followed by a series of epigenetic modifications. Little is known about the molecular machinery regulating initiation and mai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks968
更新日期:2013-01-07 00:00:00
abstract::Numerous examples exist of how disrupting the actions of physiological regulators of blood cell development yields hematologic malignancies. The master regulator of hematopoietic stem/progenitor cells GATA-2 was cloned almost 20 years ago, and elegant genetic analyses demonstrated its essential function to promote hem...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gks281
更新日期:2012-07-01 00:00:00
abstract::REDUCE is a motif-based regression method for microarray analysis. The only required inputs are (i) a single genome-wide set of absolute or relative mRNA abundances and (ii) the DNA sequence of the regulatory region associated with each gene that is probed. Currently supported organisms are yeast, worm and fly; it is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg630
更新日期:2003-07-01 00:00:00
abstract::Aminoglycosides antibiotics negate dissociation and recycling of the bacterial ribosome's subunits by binding to Helix 69 (H69) of 23S rRNA. The differential binding of various aminoglycosides to the chemically synthesized terminal domains of the Escherichia coli and human H69 has been characterized using spectroscopy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1253
更新日期:2010-05-01 00:00:00
abstract::The major immediate early regulatory region of human cytomegalovirus (HCMV) has a complex set of DNA sites through which both cellular and viral factors coordinately regulate immediate early gene expression. In undifferentiated human teratocarcinoma (T2) cells we have previously shown that major immediate early gene e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.8.1767
更新日期:1991-04-25 00:00:00
abstract::Splicing of mammalian introns requires that the intron possess at least 80 nucleotides. This length requirement presumably reflects the constraints of accommodating multiple snRNPs simultaneously in the same intron. In the free-living nematode, C. elegans, introns typically are 45 to 55 nucleotides in length. In this ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.1.143
更新日期:1990-01-11 00:00:00
abstract::Next-generation sequencing is excellently suited to evaluate the abundance of mRNAs to study gene expression. Here we compare two alternative technologies, cap analysis of gene expression (CAGE) and serial analysis of gene expression (SAGE), for the same RNA samples. Along with quantifying gene expression levels, CAGE...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq602
更新日期:2010-09-01 00:00:00
abstract::GAP-43 is a membrane phosphoprotein that is important for the development and plasticity of neural connections. In undifferentiated PC12 pheochromocytoma cells, GAP-43 mRNA degrades rapidly ( t = 5 h), but becomes stable when cells are treated with nerve growth factor. To identify trans- acting factors that may influe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.6.1281
更新日期:1997-03-15 00:00:00
abstract::The chloroplast ribosomal protein CS1 is an essential component of the plastids translational machinery involved in translation initiation. Southern analysis suggests that the corresponding nuclear gene is present in one copy in the spinach genome. We have isolated and sequenced the gene (rps1) to study its expression...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.16.4153
更新日期:1992-08-25 00:00:00
abstract::New linker phosphoramidite reagents containing a cleavable 3'-ester linkage are used for attaching the first nucleoside to the surface of a solid- phase support. Inexpensive, underivatized amino supports, such as long chain alkylamine controlled-pore glass, can serve as universal supports. No modifications to phosphor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh222
更新日期:2004-01-29 00:00:00
abstract::Previous studies have shown that the yeast Candida albicans encodes a unique seryl-tRNA(CAG) that should decode the leucine codon CUG as serine. However, in vitro translation of several different CUG-containing mRNAs in the presence of this unusual seryl-tRNA(CAG) result in an apparent increase in the molecular weight...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.9.1481
更新日期:1995-05-11 00:00:00