Abstract：
:The RosettaDesign server identifies low energy amino acid sequences for target protein structures (http://rosettadesign.med.unc.edu). The client provides the backbone coordinates of the target structure and specifies which residues to design. The server returns to the client the sequences, coordinates and energies of the designed proteins. The simulations are performed using the design module of the Rosetta program (RosettaDesign). RosettaDesign uses Monte Carlo optimization with simulated annealing to search for amino acids that pack well on the target structure and satisfy hydrogen bonding potential. RosettaDesign has been experimentally validated and has been used previously to stabilize naturally occurring proteins and design a novel protein structure.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Liu Y,Kuhlman Bdoi
10.1093/nar/gkl163subject
Has Abstractpub_date
2006-07-01 00:00:00pages
W235-8issue
Web Server issueeissn
0305-1048issn
1362-4962pii
34/suppl_2/W235journal_volume
34pub_type
杂志文章abstract：:PIWI-interacting RNAs (piRNAs) comprise a class of small RNAs best known for suppressing transposable elements in germline tissues. The vector mosquito Aedes aegypti encodes seven PIWI genes, four of which are somatically expressed. This somatic piRNA pathway generates piRNAs from viral RNA during infection with cytop...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1266
更新日期：2019-03-18 00:00:00
abstract：:We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky024
更新日期：2018-02-28 00:00:00
abstract：:The interactions between beef tRNATrp with avian myeloblastosis reverse transcriptase have been studied by statistical chemical modifications of phosphate (ethylnitrosourea) and cytidine (dimethyl sulfate) residues, as well as by digestion of complexed tRNA by Cobra venom nuclease and Neurospora crassa endonuclease. R...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.5.2259
更新日期：1984-03-12 00:00:00
abstract：:We describe conditions for producing uninterrupted expanded CTG repeats consisting of up to 2000 repeats using 29 DNA polymerase. Previously, generation of such repeats was hindered by CTG repeat instability in plasmid vectors maintained in Escherichia coli and poor in vitro ligation of CTG repeat concatemers due to s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn025
更新日期：2008-03-01 00:00:00
abstract：:RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions (UTRs). Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl1036
更新日期：2007-01-01 00:00:00
abstract：:Human telomerase is a ribonucleoprotein which uses its internal RNA moiety as a template for telomeric DNA synthesis. This enzyme is up-regulated in most malignant tumors and is therefore considered as a possible cancer target. Here we examined the effects of differently modified oligomers on telomeraseactivity from H...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.4.1152
更新日期：1999-02-15 00:00:00
abstract：:Enzymes that form transient DNA-protein covalent complexes are targets for several potent classes of drugs used to treat infectious disease and cancer, making it important to establish robust and rapid procedures for analysis of these complexes. We report a method for isolation of DNA-protein adducts and their identif...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku490
更新日期：2014-07-01 00:00:00
abstract：:mRNA deadenylation is under the control of cis-acting regulatory elements, which include AU-rich elements (AREs) and microRNA (miRNA) targeting sites, within the 3' untranslated region (3' UTRs) of eukaryotic mRNAs. Deadenylases promote miRNA-induced mRNA decay through their interaction with miRNA-induced silencing co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv959
更新日期：2015-12-15 00:00:00
abstract：:The synthesis of 1-(beta-D-2'-deoxyribosyl)-2-pyrimidinone (dK) and its 5-methyl derivative (d5) from 2'-deoxycytidine or 2'-deoxythymidine, respectively, via silver oxide oxidation of 4-hydrazinopyrimidines is described. The necessary hydrazine substituted pyrimidine nucleosides have been prepared by transamination o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.6.2261
更新日期：1989-03-25 00:00:00
abstract：:The environmental carcinogen benzo[a]pyrene (BP) is metabolized to reactive diol epoxides that bind to cellular DNA by predominantly forming N2-guanine adducts (G*). Mutation hotspots for these adducts are frequently found in 5'- ... GG ... dinucleotide sequences, but their origins are poorly understood. Here we used ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm022
更新日期：2007-01-01 00:00:00
abstract：:MeCP2 is a methyl-CpG binding protein that can repress transcription of nearby genes. In humans, mutations in the MECP2 gene are the major cause of Rett syndrome. By searching expressed sequence tag (EST) databases we have found a novel MeCP2 splice isoform (MeCP2alpha) which encodes a distinct N-terminus. We demonstr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh349
更新日期：2004-03-19 00:00:00
abstract：:Post-translational modifications (such as ubiquitination) of clock proteins are critical in maintaining the precision and robustness of the evolutionarily conserved circadian clock. Ubiquitination of the core clock transcription factor BMAL1 (brain and muscle Arnt-like 1) has recently been reported. However, it remain...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku225
更新日期：2014-05-01 00:00:00
abstract：:African trypanosomes are extracellular protozoan parasites that are transmitted from one mammalian host to the next by tsetse flies. Bloodstream forms express variant surface glycoprotein (VSG); the tsetse fly (procyclic) forms express instead the procyclic acidic repetitive protein (PARP). PARP mRNA is abundant in pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.7.1202
更新日期：1996-04-01 00:00:00
abstract：:In general, synthetic RNA transcripts corresponding to the 3' ends of Saccharomyces cerevisiae genes appear to be accurately cleaved and polyadenylated in vitro under appropriate conditions in yeast cell extracts. Initially, however, the endpoints observed in vitro for the GAL7 gene failed to correlate adequately with...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.13.3683
更新日期：1991-07-11 00:00:00
abstract：:Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we used enha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1055
更新日期：2020-12-02 00:00:00
abstract：:A new integrated image analysis package with quantitative quality control schemes is described for cDNA microarray technology. The package employs an iterative algorithm that utilizes both intensity characteristics and spatial information of the spots on a microarray image for signal-background segmentation and define...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.15.e75
更新日期：2001-08-01 00:00:00
abstract：:RNA silencing is an evolutionarily conserved mechanism triggered by double-stranded RNA that is processed into 21- to 24-nt small interfering (si)RNA or micro (mi)RNA by RNaseIII-like enzymes called Dicers. Gene regulations by RNA silencing have fundamental implications in a large number of biological processes that i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku422
更新日期：2014-07-01 00:00:00
abstract：:We report the use of an engineered ribozyme to produce a circular human exon in vitro. Specifically, we have designed a derivative of a yeast self-splicing group II intron that is able to catalyze the formation of a circular exon encoding the first kringle domain (K1) of the human tissue plasminogen activator protein....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.24.5085
更新日期：1997-12-15 00:00:00
abstract：:Extreme overloading of HPLC columns with sample can create a condition of binding site saturation causing competition and displacement among solutes during column elution. This has been termed solute-displacement chromatography (SD-HPLC). We present an example of this phenomenon for the preparative fractionation and p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.12.2913
更新日期：1993-06-25 00:00:00
abstract：:Cadmium (Cd2+) is a known carcinogen that inactivates the DNA mismatch repair (MMR) pathway. In this study, we have tested the effect of Cd2+ exposure on the enzymatic activity of the mismatch binding complex MSH2-MSH6. Our results indicate that Cd2+ is highly inhibitory to the ATP binding and hydrolysis activities of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki291
更新日期：2005-03-03 00:00:00
abstract：:The conformations of supercoiled (sc) DNA and linear DNA bound to polylysine (PL)-coated mica were investigated by scanning force microscopy (SFM) in solution. From the polymer statistical analysis of linear DNA, we could distinguish between re-arrangements or trapping of the DNA on the surface. Conditions of re-arran...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng137
更新日期：2003-11-15 00:00:00
abstract：:PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set com...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.1.61
更新日期：2001-01-01 00:00:00
abstract：:RNA polymerase III recognizes and pauses at its terminator, an oligo(dT) tract in non-template DNA, terminates 3' oligo(rU) synthesis within this sequence, and releases the RNA. The pol III subunit Rpc11p (C11) mediates RNA 3'-5' cleavage in the catalytic center of pol III during pausing. The amino and carboxyl region...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr182
更新日期：2011-08-01 00:00:00
abstract：:Pseudogenes are copies of genes that cannot produce a protein. They can be detected from disruptions to their apparent coding sequence, caused by frameshifts and premature stop codons. They are classed as either processed pseudogenes (made by reverse transcription from an mRNA) or duplicated pseudogenes, arising from ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg169
更新日期：2003-02-01 00:00:00
abstract：:Complex carbohydrates are known as mediators of complex cellular events. Concerning their structural diversity, their potential of information content is several orders of magnitude higher in a short sequence than any other biological macromolecule. SWEET-DB (http://www.dkfz.de/spec2/sweetdb/) is an attempt to use mod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.405
更新日期：2002-01-01 00:00:00
abstract：:PRED(BALB/c) is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2(d) class I (H2-K(d), H2-L(d) and H2-D(d)) and class II (I-E(d) and I-A(d)) molecules. The p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki479
更新日期：2005-07-01 00:00:00
abstract：:Highly conserved sequences present at an identical position near the 3' ends of eukaryotic and prokaryotic 5S rRNAs are complementary to the 5' strand of the m2(6)A hairpin structure near the 3' ends of 18S rRNA and 16S rRNA, respectively. The extent of base-pairing and the calculated stabilities of the hybrids that c...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/7.7.1913
更新日期：1979-12-11 00:00:00
abstract：:The TPA-inducible transcription factor AP-1, consisting of homo- or hetero-dimers of members of the Jun- and Fos-families, regulates transcription of a wide variety of genes containing the TPA response element (TRE). In P19 embryonal carcinoma (EC) cells, Jun D is the only component of AP-1 expressed, while in these c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.1.125
更新日期：1992-01-11 00:00:00
abstract：:Structural Maintenance of Chromosomes (SMC) proteins are vital for a wide range of processes including chromosome structure and dynamics, gene regulation and DNA repair. Eukaryotes have three SMC complexes, consisting of heterodimeric pairs of six different SMC proteins along with several specific regulatory subunits....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq038
更新日期：2010-06-01 00:00:00
abstract：:We have used in vitro transcription in isolated pea nuclei to determine whether the expression of genes for the seed storage proteins legumin and vicilin is regulated transcriptionally or post-transcriptionally in response to changing sulfur status in the developing seed. During the first 48 h of recovery from S defic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.3.999
更新日期：1985-02-11 00:00:00
