Abstract:
:The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, searching algorithms, data formats, data content, auxillary information, and validation techniques, as well as, of course, an increase in the number of holdings. It provides a site (http://pcddb.cryst.bbk.ac.uk) for authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. It also includes links for each entry to bioinformatics databases. The data are freely available to accessors either as single files or as complete data bank downloads. The PCDDB has found broad usage by the structural biology, bioinformatics, analytical and pharmaceutical communities, and has formed the basis for new software and methods developments.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Whitmore L,Miles AJ,Mavridis L,Janes RW,Wallace BAdoi
10.1093/nar/gkw796subject
Has Abstractpub_date
2017-01-04 00:00:00pages
D303-D307issue
D1eissn
0305-1048issn
1362-4962pii
gkw796journal_volume
45pub_type
杂志文章abstract::We report here the construction of engineered endonuclease database (EENdb) (http://eendb.zfgenetics.org/), a searchable database and knowledge base for customizable engineered endonucleases (EENs), including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). EENs are artificial...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1144
更新日期:2013-01-01 00:00:00
abstract::Some human cancers maintain their telomeres using the alternative lengthening of telomeres (ALT) mechanism; a process thought to involve recombination. Different types of recombinational telomere elongation pathways have been identified in yeasts. In senescing yeast telomerase deletion (ter1-Delta) mutants with very s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp814
更新日期:2010-01-01 00:00:00
abstract::Endonuclease III from Escherichia coli, yeast (yNtg1p and yNtg2p) and human and E.coli endonuclease VIII have a wide substrate specificity, and recognize oxidation products of both thymine and cytosine. DNA containing single dihydrouracil (DHU) and tandem DHU lesions were used as substrates for these repair enzymes. I...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.2.407
更新日期:2001-01-15 00:00:00
abstract::Efficient strategies for precise genome editing in human-induced pluripotent cells (hiPSCs) will enable sophisticated genome engineering for research and clinical purposes. The development of programmable sequence-specific nucleases such as Transcription Activator-Like Effectors Nucleases (TALENs) and Cas9-gRNA allows...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt555
更新日期:2013-10-01 00:00:00
abstract::A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.1.57
更新日期:1986-01-10 00:00:00
abstract::We have isolated the 5'-end of the gene for the rat and human link protein by screening genomic libraries with oligonucleotides corresponding to the 5'-cDNA sequence. Several overlapping clones were isolated for the human link protein gene, while only one clone was obtained for the rat. All the clones contained a sing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.8.1933
更新日期:1991-04-25 00:00:00
abstract::Nucleic acid double helices are stabilized by hydrogen bonding and stacking forces (a combination of hydrophobic, dispersive and electrostatic forces) of the base pairs in the helix. One would predict the hydrogen bonding contributions to increase and the stacking contributions to decrease as the water activity in the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm210
更新日期:2007-01-01 00:00:00
abstract::A cDNA (2855 nt) encoding a putative cytotoxic ribonuclease (rapLR1) related to the antitumor protein onconase was cloned from a library derived from the liver of gravid female amphibian Rana pipiens. The cDNA was mainly comprised (83%) of 3' untranslated region (UTR). Secondary structure analysis predicted two unusua...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.12.2375
更新日期:2000-06-15 00:00:00
abstract::The vertebrate genome is a mosaic of regions differing dramatically in their G + C content. Those regions with a high G + C content contain the expected number of CpG dinucleotides and we propose that following methylation these have been protected from deamination by the increased stability of the surrounding DNA dup...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.14.5869
更新日期:1984-07-25 00:00:00
abstract::Fundamental aspects of the biochemistry of Type III restriction endonucleases remain unresolved despite being characterized by numerous research groups in the past decades. One such feature is the subunit stoichiometry of these hetero-oligomeric enzyme complexes, which has important implications for the reaction mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku122
更新日期:2014-04-01 00:00:00
abstract::Three clones containing both the human G gamma and A gamma globlin genes have been isolated and characterized from a library of DNA fragments generated by partial Eco RI digestion of cellular DNA using charon 4A phage as vector. Two of the clones (NY 2 and 3) are identical and have an insert of 14.0 kb. The third clon...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.5.1147
更新日期:1979-11-10 00:00:00
abstract::A novel class of RNA-binding proteins, Puf, regulates translation and RNA stability by binding to specific sequences in the 3'-untranslated region of target mRNAs. Members of this protein family share a conserved Puf domain consisting of eight 36 amino acid imperfect repeats. Here we report two Puf family member genes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf600
更新日期:2002-11-01 00:00:00
abstract::In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handf...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku123
更新日期:2014-04-01 00:00:00
abstract::Aedes aegypti mosquitoes vector several arboviruses of global health significance, including dengue viruses and chikungunya virus. RNA interference (RNAi) plays an important role in antiviral immunity, gene regulation and protection from transposable elements. Double-stranded RNA binding proteins (dsRBPs) are importan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv152
更新日期:2015-04-20 00:00:00
abstract::Restriction fragment patterns of G+C-rich satellites of sheep and goat DNA were compared. The 1,712 g/cm3 satellites of both species appear homologous, consisting of repeats 760 base pairs long and showing coincidence of position of primary+ EcoRI, BamHI and most BspRI restriction target sites. The EcoRI and BamHI end...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.1.57
更新日期:1979-01-01 00:00:00
abstract::The 5'-flanking region of the bovine prolactin gene was cloned and sequenced. The expression of chimeric gene constructs containing 5'-flanking DNA fragments from the prolactin gene joined to a reporter gene encoding human growth hormone (hGH) was examined using transiently transfected rat pituitary cells. Prolactin n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:
更新日期:1990-08-25 00:00:00
abstract::The x-ray crystal structures of two new anti-HIV compounds, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine (2'-F-dd-araA) and 9-(2,3-dideoxy-2-fluoro-beta-D-threo- pentofuranosyl)hypoxanthine (2'-F-dd-aral), have been determined at two temperatures. Both crystals are in the space group P2(1)2(1)2(1), and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.3.459
更新日期:1992-02-11 00:00:00
abstract::Structural changes of reconstituted SV 40 minichromosomes have been studied in relation to the salt concentration and addition of histone H1 by sedimentation and electron microscopy. Sedimentation data are represented as functions of the NaCl concentration and the Debye-Hückel electrostatic screening radius 1/alpha. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.11.3581
更新日期:1979-08-10 00:00:00
abstract::The androgen receptor (AR) is a member of the nuclear hormone receptor family of transcription factors that plays a critical role in regulating expression of genes involved in prostate development and transformation. Upon hormone binding, the AR associates with numerous co-regulator proteins that regulate the activati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq861
更新日期:2011-03-01 00:00:00
abstract::Oligonucleotide-mediated multiplex genome engineering is an important tool for bacterial genome editing. The efficient application of this technique requires the inactivation of the endogenous methyl-directed mismatch repair system that in turn leads to a drastically elevated genomic mutation rate and the consequent a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku105
更新日期:2014-04-01 00:00:00
abstract::An endo-exonuclease has been purified from cultured monkey (CV-1) cells. The enzyme which was purified to near homogeneity to be a 65 kDa monomeric protein. The single-strand DNase activity is endonucleolytic and nonprocessive, whereas the double-strand DNase activity is exonucleolytic and processive. The enzyme was a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.16.4355
更新日期:1992-08-25 00:00:00
abstract::In continuation with work regarding the evaluation of the energy of association of various RNA bases with various base pairs, the results of the computations of the electrostatic interaction energy of A-U base pair with four RNA bases viz. Adenine, Uracil, Guanine and Cytosine have been reported. Non bonded induced po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.17.3983
更新日期:1980-09-11 00:00:00
abstract::The Mouse Genome Database (MGD) (http://www.informatics.jax.org) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and oth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1225
更新日期:2014-01-01 00:00:00
abstract::The functionalisation of oligodeoxynucleotides and oligoribonucleotides by incorporation of 2'-amido-2'-deoxyribonucleosides, possibly containing a reporter group via the 2'-amido bond, was examined. Therefore 2'-acetamido-ribonucleosides containing a small methyl group at the 2'-amido bond were synthesized as model c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.1.51
更新日期:1995-01-11 00:00:00
abstract::The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw644
更新日期:2016-09-06 00:00:00
abstract::Software has been developed to assist RNA fingerprinting analysis. One program generates, from a DNA sequence data file, the oligonucleotides resulting from digestion of an RNA transcript labeled with any specified nucleotide(s). Oligonucleotides are sorted according to their position on the fingerprint. Expected mola...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.5.1799
更新日期:1988-03-11 00:00:00
abstract::In mammalian cells, DNA damage induces robust changes in gene expression and these changes contribute to the proper execution of cellular responses to DNA damage, including DNA repair, cell cycle arrest and apoptosis. The transcription factor E2F-1 has been suggested to play a key role in the regulation of cell cycle-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.491
更新日期:1999-01-15 00:00:00
abstract::Rad54 protein is a key member of the RAD52 epistasis group required for homologous recombination in eukaryotes. Rad54 is a duplex DNA translocase that remodels both DNA and protein-DNA complexes, and functions at multiple steps in the recombination process. Here we use biochemical criteria to demonstrate the existence...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp068
更新日期:2009-05-01 00:00:00
abstract::2'-O-(2-methoxyethyl) (2'-MOE) RNA possesses favorable pharmocokinetic properties that make it a promising option for the design of oligonucleotide drugs. Telomerase is a ribonucleoprotein that is up-regulated in many types of cancer, but its potential as a target for chemotherapy awaits the development of potent and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.8.1683
更新日期:2001-04-15 00:00:00
abstract::We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki232
更新日期:2005-02-08 00:00:00