Abstract:
:ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains 10,355,444 reliable models for domains in 2,421,920 unique protein sequences. ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server (http://salilab.org/modweb). ModBase models are available through the ModBase interface as well as the Protein Model Portal (http://www.proteinmodelportal.org/). Recently developed associated resources include the SALIGN server for multiple sequence and structure alignment (http://salilab.org/salign), the ModEval server for predicting the accuracy of protein structure models (http://salilab.org/modeval), the PCSS server for predicting which peptides bind to a given protein (http://salilab.org/pcss) and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles (http://salilab.org/foxs).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Pieper U,Webb BM,Barkan DT,Schneidman-Duhovny D,Schlessinger A,Braberg H,Yang Z,Meng EC,Pettersen EF,Huang CC,Datta RS,Sampathkumar P,Madhusudhan MS,Sjölander K,Ferrin TE,Burley SK,Sali Adoi
10.1093/nar/gkq1091subject
Has Abstractpub_date
2011-01-01 00:00:00pages
D465-74issue
Database issueeissn
0305-1048issn
1362-4962pii
gkq1091journal_volume
39pub_type
杂志文章abstract::The DNA damage response is vigorously activated by DNA double-strand breaks (DSBs). The chief mobilizer of the DSB response is the ATM protein kinase. We discovered that the COP9 signalosome (CSN) is a crucial player in the DSB response and an ATM target. CSN is a protein complex that regulates the activity of cullin ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv270
更新日期:2015-05-19 00:00:00
abstract::In neural stem cells (NSCs), the balance between stem cell maintenance and neuronal differentiation depends on cell-fate determinants such as TRIM32. Previously, we have shown that TRIM32 associates with the RNA-induced silencing complex and increases the activity of microRNAs such as Let-7a. However, the exact mechan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv138
更新日期:2015-03-11 00:00:00
abstract::The synthesis of ribosomal precursor RNA in Novikoff hepatoma (N1S1) cells is very sensitive to cordycepin (3'-dA). The synthesis of hnRNA, however, is resistant to inhibition concentrations of 3'-dA that completely block the synthesis of 45S ribosomal RNA precursor. We have examined the RNA polymerases present in the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.2.325
更新日期:1976-02-01 00:00:00
abstract::By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx859
更新日期:2017-12-15 00:00:00
abstract::Denaturing gradient gel electrophoresis (DGGE) is based upon the different melting behaviors of DNA molecules in a chemical denaturant gradient according to their sequences. This technique has recently become a widespread tool to detect mutations. The introduction of a GC-clamp enables the detection of most single bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.12.3331
更新日期:1991-06-25 00:00:00
abstract::DEAD-box helicases catalyze the non-processive unwinding of double-stranded RNA (dsRNA) at the expense of adenosine triphosphate (ATP) hydrolysis. Nucleotide and RNA binding and unwinding are mediated by the RecA domains of the helicase core, but their cooperation in these processes remains poorly understood. We there...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku747
更新日期:2014-01-01 00:00:00
abstract::We have constructed and tested several new vectors for P element-mediated gene transfer. These vectors contain restriction sites for cloning a wide variety of DNA fragments within a small, non-autonomous P element and can be used to efficiently transduce microinjected DNA sequences into the germ line chromosomes of D....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.18.6341
更新日期:1983-09-24 00:00:00
abstract::DAXX displays complex biological functions. Remarkably, DAXX overexpression is a common feature in diverse cancers, which correlates with tumorigenesis, disease progression and treatment resistance. Structurally, DAXX is modular with an N-terminal helical bundle, a docking site for many DAXX interactors (e.g. p53 and ...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkz634
更新日期:2019-09-05 00:00:00
abstract::Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw930
更新日期:2016-11-16 00:00:00
abstract::We have investigated loop-induced structural perturbation of the stem structure in hairpins d(GAATTCXnGAATTC) (X = A, T and n = 3, 4, 5 and 6) that contain an EcoRI restriction site in close proximity to the hairpin loop. Oligonucleotides containing either a T3 or a A3 loop were not hydrolyzed by the restriction enzym...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.6.1489
更新日期:1990-03-25 00:00:00
abstract::A type II restriction endonuclease, named CviJI, was isolated from a eukaryotic Chlorella-like green alga infected with the dsDNA containing virus IL-3A. CviJI is the first restriction endonuclease to recognize the sequence PuGCPy; CviJI cleaves DNA between the G and C. Methylation of the cytosine in PuGCPy sequences ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.15.6075
更新日期:1987-08-11 00:00:00
abstract::1,10-Phenanthroline-platinum(II)-ethylenediamine ( PEPt ) forms a crystalline complex with cytidine-3'-phosphate (3'-CMP) and its structure has been determined by X-ray crystallography. 3'-CMP molecules are hemiprotonated and form hydrogen-bonded pairs that stack above and below the phenanthroline-platinum(II) drug mo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.8.3649
更新日期:1984-04-25 00:00:00
abstract::The P. falciparum pPFrep20 repetitive element from the Palo Alto Uganda strain has been isolated and sequenced. The Palo Alto pPFrep20 repeat (pPFPArep20) has a clustered subtelomeric location and on chromosome 1 has been deleted from one end. Analysis of chromosome 1 from 5 other strains has revealed that pPFrep20 se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4331
更新日期:1988-05-25 00:00:00
abstract::ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl880
更新日期:2007-01-01 00:00:00
abstract::DNA methylation, the most intensively studied epigenetic modification, plays an important role in understanding the molecular basis of diseases. Furthermore, epigenome-wide association study (EWAS) provides a systematic approach to identify epigenetic variants underlying common diseases/phenotypes. However, there is n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky942
更新日期:2019-01-08 00:00:00
abstract::The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.2.555
更新日期:1988-01-25 00:00:00
abstract::Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm513
更新日期:2007-01-01 00:00:00
abstract::Late SV40 16S and 19S mRNAs were found to contain an average of three m6A residues per mRNA molecule. The methylated residues of both the viral and cellular mRNAs occur in two sequences; Gpm6ApC and (Ap)nm6ApC, where n = 1-4. More than 60% of the m6A residues in SV40 16S and 19S mRNAs occur in Gpm6ApC even though ther...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.8.2879
更新日期:1979-06-25 00:00:00
abstract::Double-stranded (ds) oligodeoxynucleotides (29mers) containing an O6-ethylguanine (O6-EtGua) flanked 5' and 3' by different bases (5'..TGT..3'; 5'..CGG..3', 5'..GGT..3'; 5'..GGG..3'; 5'..GGA..3') were synthesized to investigate the binding and repair characteristics of recombinant human O6-alkylguanine-DNA alkyltransf...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.11.2087
更新日期:1996-06-01 00:00:00
abstract::Yeast Dna2 helicase/nuclease is essential for DNA replication and assists FEN1 nuclease in processing a subset of Okazaki fragments that have long single-stranded 5' flaps. It is also involved in the maintenance of telomeres. DNA2 is a gene conserved in eukaryotes, and a putative human ortholog of yeast DNA2 (ScDNA2) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl070
更新日期:2006-04-04 00:00:00
abstract::With the recent increase in the number of mammalian genomes being sequenced, large-scale genome scans for human-specific positive selection are now possible. Selection can be inferred through phylogenetic analysis by comparing the rates of silent and replacement substitution between related species. Maximum-likelihood...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm764
更新日期:2008-01-01 00:00:00
abstract::The ability to store and interconnect all available information on proteins is crucial to modern biological research. Accordingly, the Universal Protein Resource (UniProt) plays an increasingly important role by providing a stable, comprehensive, freely accessible central resource on protein sequences and functional a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl929
更新日期:2007-01-01 00:00:00
abstract::BRCA1 expression is repressed by aberrant cytosine methylation in sporadic breast cancer. We hypothesized that aberrant cytosine methylation of the BRCA1 promoter was associated with the transcriptionally repressive effects of histone hypoacetylation and chromatin condensation. To address this question, we developed a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.17.3233
更新日期:2000-09-01 00:00:00
abstract::Among a collection of 74 aprt mutations induced by treatment of plateau phase Chinese hamster ovary CHO cells with the radiomimetic DNA double-strand cleaving agent neocarzinostatin, nine were large-scale rearrangements. Molecular analysis indicated that all nine were highly conservative, non-homologous reciprocal exc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf369
更新日期:2002-06-15 00:00:00
abstract::Periodically repeating DNA and protein elements are involved in various important biological events including genomic evolution, gene regulation, protein complex formation, and immunity. Notably, the currently used genome editing tools such as ZFNs, TALENs, and CRISPRs are also all associated with periodically repeati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky890
更新日期:2019-01-25 00:00:00
abstract::CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR inter...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1259
更新日期:2015-12-15 00:00:00
abstract::We have isolated genomic clones from Xenopus borealis representing 3 different types of histone gene cluster. We show that the major type (H1, H2B, H2A, H4, H3), present at about 60-70 copies per haploid genome (1), is tandemly reiterated with a repeat length of 15 kb. In situ hybridization to mitotic chromosomes show...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.8.3471
更新日期:1988-04-25 00:00:00
abstract::A terminator of transcription with bidirectional activity has been located between the translation termination codons of the genes tetA and orfL on Tn10. These genes are transcribed towards each other. Each orientation of the intervening sequence is shown to reduce the expression of the lacZ and galK genes when cloned...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.12.4227
更新日期:1985-06-25 00:00:00
abstract::DNA strand exchange, the central step of homologous recombination, is considered to occur approximately independently of DNA sequence content. However, certain prokaryotic and eukaryotic genomic loci display either an enhanced or reduced frequency of genetic exchange. Here we show that the Homo sapiens DNA strand exch...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl355
更新日期:2006-05-24 00:00:00
abstract::An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the map...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw026
更新日期:2016-05-05 00:00:00