Abstract:
:The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath_new) currently contains 34 287 domain structures classified into 1383 superfamilies and 3285 sequence families. Each structural family is expanded with domain sequence relatives recruited from GenBank using a variety of efficient sequence search protocols and reliable thresholds. This extended resource, known as the CATH-protein family database (CATH-PFDB) contains a total of 310 000 domain sequences classified into 26 812 sequence families. New sequence search protocols have been designed, based on these intermediate sequence libraries, to allow more regular updating of the classification. Further developments include the adaptation of a recently developed method for rapid structure comparison, based on secondary structure matching, for domain boundary assignment. The philosophy behind CATHEDRAL is the recognition of recurrent folds already classified in CATH. Benchmarking of CATHEDRAL, using manually validated domain assignments, demonstrated that 43% of domains boundaries could be completely automatically assigned. This is an improvement on a previous consensus approach for which only 10-20% of domains could be reliably processed in a completely automated fashion. Since domain boundary assignment is a significant bottleneck in the classification of new structures, CATHEDRAL will also help to increase the frequency of CATH updates.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Pearl FM,Bennett CF,Bray JE,Harrison AP,Martin N,Shepherd A,Sillitoe I,Thornton J,Orengo CAdoi
10.1093/nar/gkg062keywords:
subject
Has Abstractpub_date
2003-01-01 00:00:00pages
452-5issue
1eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::The solution structures of two 27 nt RNA hairpins and their complexes with cobalt(III)-hexammine [Co(NH(3))(6)(3+)] were determined by NMR spectroscopy. The RNA hairpins are variants of the P4 region from Escherichia coli RNase P RNA: a U-to-A mutant changing the identity of the bulged nucleotide, and a U-to-C, C-to-U...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh961
更新日期:2004-12-02 00:00:00
abstract::We have developed an effective, easy-to-use two-step system for the site-directed insertion of large genetic constructs into arbitrary positions in the Escherichia coli chromosome. The system uses lambda-Red mediated recombineering accompanied by the introduction of double-strand DNA breaks in the chromosome and a don...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1193
更新日期:2010-04-01 00:00:00
abstract::In this study we describe a novel method to investigate the RNA-RNA interactions between a small RNA and its target that we termed 'RNA walk'. The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT-PCR or real-time...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp872
更新日期:2010-01-01 00:00:00
abstract::Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky945
更新日期:2019-01-10 00:00:00
abstract::The transactivator responsive region (TAR) present in the 5'-NTR of the HIV-1 genome represents a potential target for antiretroviral intervention and a model system for the development of specific inhibitors of RNA-protein interaction. Earlier, we have shown that an anti-TAR polyamide nucleotide analog (PNA(TAR)) con...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki743
更新日期:2005-08-02 00:00:00
abstract::N7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2'-fluorine-mediated transition-state destabilz...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku554
更新日期:2014-07-01 00:00:00
abstract::Increased cytochrome P450 2E1 (CYP2E1) expression is the main cause of oxidative stress, which exacerbates alcoholic liver diseases (ALDs). Estrogen-related receptor gamma (ERRγ) induces CYP2E1 expression and contributes to enhancing alcohol-induced liver injury. Retinoic acid-related orphan receptor alpha (RORα) has ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1034
更新日期:2016-02-18 00:00:00
abstract::A DNA copy of influenza A/NT/60/68 viral RNA segment 2, corresponding to protein P1, has been cloned in the E.coli plasmid pBr322. The clone is 2341 nucleotides long and represents a full-length copy of the viral RNA. In the viral complementary (plus sense) strand there is an open reading frame that is 2271 nucleotide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.4.1335
更新日期:1982-02-25 00:00:00
abstract::Interactions between proteins bound to distant sites along a DNA molecule require bending and twisting deformations in the intervening DNA. In certain systems, the sterically allowed protein-DNA and protein-protein interactions are hypothesized to produce loops with distinct geometries that may also be thermodynamical...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn389
更新日期:2008-07-01 00:00:00
abstract::Our database on large ribosomal subunit RNA contained 334 sequences in July, 1995. All sequences in the database are aligned, taking into account secondary structure. The aligned sequences are provided, together with incorporated secondary structure information, in several computer-readable formats. These data can eas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.92
更新日期:1996-01-01 00:00:00
abstract::We have isolated and characterized DNA probes that detect homologies between the X and Y chromosomes. Clone St25 is derived from the q13-q22 region of the X chromosome and recognizes a 98% homologous sequence on the Y chromosome. Y specific fragments were present in DNAs from 5 Yq-individuals and from 4 out of 7 XX ma...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.15.5485
更新日期:1985-08-12 00:00:00
abstract::Pax-5, a member of the paired domain family of transcription factors, is a key regulator of B lymphocyte-specific transcription and differentiation. A major target of Pax-5-mediated activation is the mb-1 gene, which encodes the essential transmembrane signaling protein Ig-alpha. Pax-5 recruits three members of the Et...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg785
更新日期:2003-10-01 00:00:00
abstract::Upon growth transition of Escherichia coli cells from exponential to stationary phase, RNA polymerase is converted into at least three different forms (S1, S2 and S3), which could be separately isolated by phosphocellulose column chromatography (Ozaki et al., 1991 (2)). Here, the promoter selectivity of these three st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.2.257
更新日期:1992-01-25 00:00:00
abstract::Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.12.2212
更新日期:1995-06-25 00:00:00
abstract::The Kruppel-like factor 5 (KLF5/IKLF) belongs to the Kruppel family of genes which bind GC-rich DNA elements and activate or repress their target genes in a promoter context and/or cellular environment-dependent manner. In the present study, we used the Gal4 fusion assay system to characterize the mechanism of transac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg310
更新日期:2003-04-15 00:00:00
abstract::5' strand resection at DNA double strand breaks (DSBs) is critical for homologous recombination (HR) and genomic stability. Here we develop a novel method to quantitatively measure single-stranded DNA intermediates in human cells and find that the 5' strand at endonuclease-generated break sites is resected up to 3.5 k...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1309
更新日期:2014-02-01 00:00:00
abstract::We have examined the expression and structure of several genes belonging to two classes of vegetative specific genes of the simple eukaryote, Dictyostelium discoideum. In amebae grown on bacteria, deactivation of all vegetative specific genes occurred at the onset of development and very little mRNA exists by 8 to 10 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.23.9679
更新日期:1989-12-11 00:00:00
abstract::Previous studies have implicated the DE-1 (-111/-106) and alpha A-CRYBP1 (-66/-57) sites for activity of the mouse alpha A-crystallin promoter in transiently transfected lens cells. Here we have used the bacterial chloramphenicol acetyltransferase (CAT) reporter gene to test the functional importance of the putative D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.11.2633
更新日期:1993-06-11 00:00:00
abstract::Hexokinase 2 is an essential factor for signalling repression through the Saccharomyces cerevisiae high-glucose sensing pathway. The main regulatory mechanism that controls the HXK2 gene expression in yeast is mediated by the Rgt1 and Med8 transcription factors, which repress HXK2 expression in low-glucose containing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl028
更新日期:2006-03-09 00:00:00
abstract::Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alterna...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1271
更新日期:2013-02-01 00:00:00
abstract::RNA secondary structures, e.g. stem-loops that are often found at the 5' and 3' ends of mRNAs, are in many cases known to be crucial for transcript stability but their role in prolonging the lifetime of transcripts remains elusive. In this study we show for an essential RNA-stabilizing stem-loop at the 5' end of rbcL ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki760
更新日期:2005-08-22 00:00:00
abstract::A dnaB-like protein from P. aeruginosa was purified to near homogeneity using as an assay the immunoprecipitation by E. coli dnaB antiserum in a solid-phase. In the chromatographic characteristics including the affinity to immobilized ATP the dnaB-like protein of P. aeruginosa is similar to the dnaB protein of E. coli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.2.385
更新日期:1987-01-26 00:00:00
abstract::Two residues are invariant in all bZip basic regions: asparagine -18 and arginine -10 (we define the first leucine of the leucine zipper of GCN4 as +1). X-ray structures of two specific GCN4-DNA complexes (Ellenberger et al., Cell, 71, 1223-1237, 1992; König & Richmond, J. Mol. Biol., 233, 139-154, 1993) demonstrate t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.21.4395
更新日期:1994-10-25 00:00:00
abstract::Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; 'tsRNA') or cis-backsplicing (circular RNA; 'circRNA'). While numerous circRNAs have been detected in various species, tsRNAs remain largely uninvestigated. Here, we utilize integrative transcriptome sequencing of p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky032
更新日期:2018-04-20 00:00:00
abstract::At either end of the nopaline Ti-plasmid T-region resides a copy of a 25 bp repeated element. The normal T-DNA endpoint is 1 bp internal of the right copy, with the transcription initiation site of the nopaline synthase (nos) gene being approximately 300 bp away in the same direction. Here we describe results which de...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.15.6031
更新日期:1984-08-10 00:00:00
abstract::The agents daunomycin, ethidium bromide, distamycin A and cytochrome c inhibit DNA dependent DNA polymerase I (E. coli) reaction competitively to DNA. The influence of these template inactivators on the binding of DNA polymerase to native as well as denatured DNA has been determined by affinity chromatography. Cytochr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.1.63
更新日期:1974-01-01 00:00:00
abstract::Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiRe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx610
更新日期:2017-09-06 00:00:00
abstract::The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called 'K*Sync', in which alignments are generated by dynamic program...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl480
更新日期:2006-01-01 00:00:00
abstract::Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for diva...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1175
更新日期:2017-01-25 00:00:00
abstract::Exposure of Schizosaccharomyces pombe cells to UV light results in increased uvi15(+) gene expression at both the mRNA and protein levels, leading to elevated cell survival. This UV-induced expression of the uvi15(+) gene was reduced in Deltasty1 and Deltawis1 cells lacking the stress-activated protein kinase pathway,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.17.3392
更新日期:2000-09-01 00:00:00