Abstract:
:The Protein Folding Database (PFD) is a publicly accessible repository of thermodynamic and kinetic protein folding data. Here we describe the first major revision of this work, featuring extensive restructuring that conforms to standards set out by the recently formed International Foldeomics Consortium. The database now adopts standards for data acquisition, analysis and reporting proposed by the consortium, which will facilitate the comparison of folding rates, energies and structure across diverse sets of proteins. Data can now be easily deposited using a rich set of deposition tools. Enhanced search tools allow sophisticated searching and graphical data analysis affords simple data analysis online. PFD can be accessed freely at http://www.foldeomics.org/pfd/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Fulton KF,Bate MA,Faux NG,Mahmood K,Betts C,Buckle AMdoi
10.1093/nar/gkl1007subject
Has Abstractpub_date
2007-01-01 00:00:00pages
D304-7issue
Database issueeissn
0305-1048issn
1362-4962pii
gkl1007journal_volume
35pub_type
杂志文章abstract::The base pairing properties of oligonucleotide duplexes containing 8-aza-7-deaza-2'-deoxyisoguanosine, its 7-bromo or its 7-iodo derivative are described. The nucleosides were synthesized on a convergent route, protected and converted into phosphoramidites. Oligonucleotides were prepared on a solid-phase and were hybr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg926
更新日期:2003-12-15 00:00:00
abstract::In addition to being a hallmark at active genes, histone variant H3.3 is deposited by ATRX at repressive chromatin regions, including the telomeres. It is unclear how H3.3 promotes heterochromatin assembly. We show that H3.3 is targeted for K9 trimethylation to establish a heterochromatic state enriched in trimethylat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv847
更新日期:2015-12-02 00:00:00
abstract::We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn524
更新日期:2008-10-01 00:00:00
abstract::Several authors have suggested or inferred that modest changes in microRNA expression can potentiate or impinge on their capacity to mediate gene repression, and that doing so could play a significant role in diseases. Such interpretations are based on several assumptions, namely: (i) changes in microRNA expression co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv720
更新日期:2015-09-03 00:00:00
abstract::DNA double-strand breaks are repaired by end-joining or homologous recombination. A key-committing step of recombination is DNA end resection. In resection, phosphorylated CtIP first promotes the endonuclease of MRE11-RAD50-NBS1 (MRN). Subsequently, CtIP also stimulates the WRN/BLM-DNA2 pathway, coordinating thus both...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa273
更新日期:2020-06-04 00:00:00
abstract::Invertebrate RNA viruses are targets of the host RNA interference (RNAi) pathway, which limits virus infection by degrading viral RNA substrates. Several insect RNA viruses encode suppressor proteins to counteract this antiviral response. We recently demonstrated that the dsDNA virus Invertebrate iridescent virus 6 (I...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku910
更新日期:2014-10-29 00:00:00
abstract::The detailed conformational features and dynamics of the naturally occurring deoxyribotrinucleoside diphosphates d-TpTpT and d-TpTpC have been investigated at 20 degrees C and 80 degrees C in aqueous solution by nuclear magnetic resonance spectroscopy. The observed NMR parameters indicate that the conformational prope...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.11.4399
更新日期:1978-11-01 00:00:00
abstract::Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku269
更新日期:2014-06-01 00:00:00
abstract::Various in vivo mutagenesis methods have been developed to facilitate fast and efficient continuous evolution of proteins in cells. However, they either modify the DNA region that does not match the target gene, or suffer from low mutation rates. Here, we report a mutator, eMutaT7 (enhanced MutaT7), with very fast in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1231
更新日期:2021-01-06 00:00:00
abstract::RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. How...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx388
更新日期:2017-07-07 00:00:00
abstract::The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1133
更新日期:2017-01-04 00:00:00
abstract::The behaviour of highly purified bacterial expressed rat O6-methylguanine-DNA methyltransferase (MGMT) towards the repair of CGCm6GAGCTCGCG and CGCe6GAGCTCGCG (km6G/ke6G = 1.45, where k is the second order repair rate constant determined, m6G and e6G are O6-methyl and O6-ethylguanine) is similar to that of E. coli 39k...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.9.1613
更新日期:1994-05-11 00:00:00
abstract::Translation initiation of eukaryotic mRNAs generally occurs by cap-dependent ribosome scanning. However, certain mRNAs contain internal ribosome entry sites (IRES) allowing cap-independent translation. Several of these IRES-competent transcripts and their corresponding proteins are involved in tumourigenesis. This stu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm096
更新日期:2007-01-01 00:00:00
abstract::Aspartic acid residues comprising the -D-(aa) n -Y-L-D-D- DNA polymerase active site triad of reverse transcriptase from the Saccharomyces cerevisiae long terminal repeat-retrotransposon Ty3 (Asp151, Asp213 and Asp214) were evaluated via site-directed mutagenesis. An Asp151-->Glu substitution showed a dramatic decreas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki150
更新日期:2005-01-12 00:00:00
abstract::The mRNA encoding repressor cI of phage lambda is the only known E. coli message which starts directly with the initiation AUG codon. The ability of in vitro synthesized cI mRNA fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. In the presence of tRNA(Met)f, th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.3.563
更新日期:1992-02-11 00:00:00
abstract::The ribosomal frameshifting signal of the mouse embryonal carcinoma differentiation regulated (Edr) gene represents the sole documented example of programmed -1 frameshifting in mammalian cellular genes [Shigemoto,K., Brennan,J., Walls,E,. Watson,C.J., Stott,D., Rigby,P.W. and Reith,A.D. (2001), Nucleic Acids Res., 29...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki299
更新日期:2005-03-14 00:00:00
abstract::The modified nucleoside, 7-(4,5-cis-dihydroxy-1-cyclopenten-3-yl-aminomethyl)-7-deazaguanosine, designated as Q, and its derivative, Q*, were found in tRNA's from various organisms, including several mammalian tissues, other animals such as starfish, lingula and hagfish, and wheat germ. Q isolated from rat liver tRNA ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.10.1931
更新日期:1975-10-01 00:00:00
abstract::The HIV RT and Protease Sequence Database is an online relational database that catalogs evolutionary and drug-related human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease sequence variation (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protea...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.346
更新日期:2000-01-01 00:00:00
abstract::Transcriptional repression of pathogen defense-related genes is essential for plant growth and development. Several proteins are known to be involved in the transcriptional regulation of plant defense responses. However, mechanisms by which expression of defense-related genes are regulated by repressor proteins are po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks683
更新日期:2012-10-01 00:00:00
abstract::Currently transgenic frog embryos are generated using restriction-enzyme-mediated integration (REMI) on decondensed sperm nuclei followed by nuclear transplantation into unfertilized eggs. We have developed a simplified version of this protocol that has the potential to increase the numbers of normally developing tran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.4.e12
更新日期:2000-02-15 00:00:00
abstract::Transfer ribonucleic acids were isolated from mitochondria of bovine heart and aminoacylated in vitro by a crude mitochondrial enzyme. Ser-tRNASerUCN and Ser-tRNASerAGY were isolated and characterized by partial sequencing. Although these tRNAs possess unique structural features not found in any bacterial tRNA, they f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.18.7175
更新日期:1986-09-25 00:00:00
abstract::The HAMSTeRS WWW site was set up in 1996 in order to facilitate easy access to, and aid understanding of, the causes of haemophilia A at the molecular level; previously, the first and second text editions of the database have been published in Nucleic Acids Research. This report describes the facilities originally ava...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.1.128
更新日期:1997-01-01 00:00:00
abstract::The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.2801
更新日期:1978-08-01 00:00:00
abstract::Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh476
更新日期:2004-07-01 00:00:00
abstract::Horizontally acquired genes are typically regulated by ancestral regulators. This regulation enables expression of horizontally acquired genes to be coordinated with that of preexisting genes. Here, we report a singular example of the opposite regulation: a horizontally acquired gene that controls an ancestral regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa813
更新日期:2020-11-04 00:00:00
abstract::Cooperative hybridization has been used to establish physical linkage between two loci on a DNA strand. Linkage was detected by hybridization to a new type of high-density oligonucleotide array. Each synthesis location on the array contains a mixture of two different probe sequences. Each of the two probes can hybridi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.6.1485
更新日期:1999-03-15 00:00:00
abstract::Biophysical properties of DNA such as its longitudinal and torsional persistence length govern many processes and phenomena in biology, DNA nanotechnology and biotechnology. It has, for example, long been known that the circularization efficiency of short DNA fragments shows a periodic pattern where fragments with int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1238
更新日期:2018-01-25 00:00:00
abstract::The diverse localization of transcripts in cells suggests that there are many specific RNA-protein interactions that have yet to be identified. Progress has been limited, however, by the lack of a robust method to detect and isolate the RNA-binding proteins. Here we describe the use of an RNA aptamer, scaffolded to a ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1316
更新日期:2011-04-01 00:00:00
abstract::Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction data...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl783
更新日期:2007-01-01 00:00:00
abstract::Potential pathways that could account for observed rapid rates of transcription reinitiation were explored. A nuclear extract system was established in which reinitiation rates were observed to be kinetically facilitated and in which the rate was sensitive to TATA box mutation. Kinetic facilitation of functional compl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.3.831
更新日期:1999-02-01 00:00:00