Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications.

abstract：:Transcription and translation are coupled in bacteria, meaning that translation takes place co-transcriptionally. During transcription-translation, both machineries mutually affect each others' functions, which is important for regulation of gene expression. Analysis of interactions between RNA polymerase (RNAP) and t...

journal_title：Nucleic acids research

authors： Castro-Roa D,Zenkin N

更新日期：2012-03-01 00:00:00

abstract：:We have isolated from a single human liver cDNA library two clones which are highly homologous (78% over the coding region) to the major phenobarbital-inducible P450 from rat (P450IIB1). This is the first direct demonstration of the presence of the P450IIB gene subfamily in humans. This subfamily is much less extensiv...

journal_title：Nucleic acids research

authors： Miles JS,Spurr NK,Gough AC,Jowett T,McLaren AW,Brook JD,Wolf CR

更新日期：1988-07-11 00:00:00

abstract：:Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we discover an HRP2-DPF3a-BAF epigenetic pathway that coordinates methylated histone H3 ly...

journal_title：Nucleic acids research

authors： Zhu X,Lan B,Yi X,He C,Dang L,Zhou X,Lu Y,Sun Y,Liu Z,Bai X,Zhang K,Li B,Li MJ,Chen Y,Zhang L

更新日期：2020-07-09 00:00:00

abstract：:A 14 kb maize DNA fragment carrying nuclear rRNA genes and spacer regions was isolated and characterised by restriction enzyme mapping. A complete 3020 bp long external spacer region was sequenced and revealed 9 tandemly arranged 200 bp long repeat units with high homology. The repeat units lie upstream from two promi...

journal_title：Nucleic acids research

authors： Toloczyki C,Feix G

更新日期：1986-06-25 00:00:00

abstract：:The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAS...

journal_title：Nucleic acids research

authors： Alva V,Nam SZ,Söding J,Lupas AN

更新日期：2016-07-08 00:00:00

abstract：:The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using...

journal_title：Nucleic acids research

authors： Ananko EA,Podkolodny NL,Stepanenko IL,Podkolodnaya OA,Rasskazov DA,Miginsky DS,Likhoshvai VA,Ratushny AV,Podkolodnaya NN,Kolchanov NA

更新日期：2005-01-01 00:00:00

abstract：:It has been inferred from DNA sequence analyses that in echinoderm mitochondria not only the usual asparagine codons AAU and AAC, but also the usual lysine codon AAA, are translated as asparagine by a single mitochondrial (mt) tRNAAsn with the anticodon GUU. Nucleotide sequencing of starfish mt tRNAAsn revealed that t...

journal_title：Nucleic acids research

authors： Tomita K,Ueda T,Watanabe K

更新日期：1999-04-01 00:00:00

abstract：:The nucleotide sequence of the control region of the divergent argECBH operon has been established in the wild type and in mutants affecting expression of these genes. The argE and argCBH promoters face each other and overlap with an operator region containing two domains which may act as distinct repressor binding si...

journal_title：Nucleic acids research

authors： Piette J,Cunin R,Boyen A,Charlier D,Crabeel M,Van Vliet F,Glansdorff N,Squires C,Squires CL

更新日期：1982-12-20 00:00:00

abstract：:In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utili...

journal_title：Nucleic acids research

authors： Wheeler DL,Barrett T,Benson DA,Bryant SH,Canese K,Chetvernin V,Church DM,DiCuccio M,Edgar R,Federhen S,Geer LY,Helmberg W,Kapustin Y,Kenton DL,Khovayko O,Lipman DJ,Madden TL,Maglott DR,Ostell J,Pruitt KD,Schuler G

更新日期：2006-01-01 00:00:00

abstract：:A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino a...

journal_title：Nucleic acids research

authors： Harrison JG,Balasubramanian S

更新日期：1998-07-01 00:00:00

abstract：:Bursts of free radicals produced by ionization of water in close vicinity to DNA can produce clusters of opposed DNA lesions and these are termed multiply damaged sites (MDS). How MDS are processed by the Escherichia coli DNA glycosylases, endonuclease (endo) III and endo VIII, which recognize oxidized pyrimidines, is...

journal_title：Nucleic acids research

authors： Harrison L,Hatahet Z,Purmal AA,Wallace SS

更新日期：1998-02-15 00:00:00

abstract：:eIF4E-binding proteins (4E-BPs) regulate translation of mRNAs in eukaryotes. However the extent to which specific mRNA targets are regulated by 4E-BPs remains unknown. We performed translational profiling by microarray analysis of polysome and monosome associated mRNAs in wild-type and mutant cells to identify mRNAs i...

journal_title：Nucleic acids research

authors： Cridge AG,Castelli LM,Smirnova JB,Selley JN,Rowe W,Hubbard SJ,McCarthy JE,Ashe MP,Grant CM,Pavitt GD

更新日期：2010-12-01 00:00:00

abstract：:A number of regulatory nascent peptides have been shown to regulate gene expression by causing programmed ribosome stalling during translation. Nascent peptide emerges from the ribosome through the exit tunnel, and one-third of the way along which β-loop structures of ribosomal proteins uL4 and uL22 protrude into the ...

journal_title：Nucleic acids research

authors： Takamatsu S,Ohashi Y,Onoue N,Tajima Y,Imamichi T,Yonezawa S,Morimoto K,Onouchi H,Yamashita Y,Naito S

更新日期：2020-02-28 00:00:00

abstract：:During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is ...

journal_title：Nucleic acids research

authors： Bleda M,Tarraga J,de Maria A,Salavert F,Garcia-Alonso L,Celma M,Martin A,Dopazo J,Medina I

更新日期：2012-07-01 00:00:00

abstract：:A synthetic gene for somatomedin C, a human growth factor, has been assembled by a single ligation of 23 oligodeoxyribonucleotides, which were chemically synthesized by an improved solid phase phosphotriester method. ...

journal_title：Nucleic acids research

authors： Sproat BS,Gait MJ

更新日期：1985-04-25 00:00:00

abstract：:A lac promotor mutant was constructed by filling in the protruding ends of the HpaII site located within the lac promotor. The mutation, named M42, is a two base pair insertion that changes the distance between the -10 and -35 regions from 18 to 20 residues. The activity of the mutant promotor measured in vivo is 15% ...

journal_title：Nucleic acids research

authors： Mandecki W,Reznikoff WS

更新日期：1982-02-11 00:00:00

abstract：:We previously reported that O4-alkyl dTTPs could replace, for short times, dTTP in polymer synthesis [Singer et al., PNAS 83, 26-32, 1986]. The reasons for such early termination of synthesis could be either proofreading or the eventual formation of weakly paired primer termini. Utilizing the known 3'----5' exonucleol...

journal_title：Nucleic acids research

authors： Singer B

更新日期：1986-08-26 00:00:00

abstract：:Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro /in silico screening we identified RNA-bindi...

journal_title：Nucleic acids research

authors： Marchese D,Botta-Orfila T,Cirillo D,Rodriguez JA,Livi CM,Fernández-Santiago R,Ezquerra M,Martí MJ,Bechara E,Tartaglia GG,Catalan MSA Registry (CMSAR).

更新日期：2017-12-15 00:00:00

abstract：:The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging probl...

journal_title：Nucleic acids research

authors： Rho M,Tang H,Ye Y

更新日期：2010-11-01 00:00:00

abstract：:The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3'-5' exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in ...

journal_title：Nucleic acids research

authors： Koc KN,Stodola JL,Burgers PM,Galletto R

更新日期：2015-04-30 00:00:00

abstract：:The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries...

journal_title：Nucleic acids research

authors： Maheswari U,Mock T,Armbrust EV,Bowler C

更新日期：2009-01-01 00:00:00

abstract：:Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3' bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome v...

journal_title：Nucleic acids research

authors： Welch JD,Hu Y,Prins JF

更新日期：2016-05-05 00:00:00

abstract：:The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts the alignments of a number of genomes computed by our group, allowing ...

journal_title：Nucleic acids research

authors： Brudno M,Poliakov A,Minovitsky S,Ratnere I,Dubchak I

更新日期：2007-07-01 00:00:00

abstract：:BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and mol...

journal_title：Nucleic acids research

authors： Schomburg I,Chang A,Ebeling C,Gremse M,Heldt C,Huhn G,Schomburg D

更新日期：2004-01-01 00:00:00

abstract：:The availability of the complete sequence of the Saccharomyces cerevisiae genome has allowed a comprehensive analysis of the genes encoding cytoplasmic ribosomal proteins in this organism. On the basis of this complete inventory a new nomenclature for the yeast ribosomal proteins is presented. ...

journal_title：Nucleic acids research

authors： Mager WH,Planta RJ,Ballesta JG,Lee JC,Mizuta K,Suzuki K,Warner JR,Woolford J

更新日期：1997-12-15 00:00:00

abstract：:OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the al...

journal_title：Nucleic acids research

authors： Altenhoff AM,Schneider A,Gonnet GH,Dessimoz C

更新日期：2011-01-01 00:00:00

abstract：:The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new feat...

journal_title：Nucleic acids research

authors： Altenhoff AM,Glover NM,Train CM,Kaleb K,Warwick Vesztrocy A,Dylus D,de Farias TM,Zile K,Stevenson C,Long J,Redestig H,Gonnet GH,Dessimoz C

更新日期：2018-01-04 00:00:00

abstract：:Coralyne is a small crescent-shaped molecule known to intercalate duplex and triplex DNA. We report that coralyne can cause the complete and irreversible disproportionation of duplex poly(dT)*poly(dA). That is, coralyne causes the strands of duplex poly(dT)*poly(dA) to repartition into equal molar equivalents of tripl...

journal_title：Nucleic acids research

authors： Polak M,Hud NV

更新日期：2002-02-15 00:00:00

abstract：:Triple helix-forming oligonucleotides covalently linked to topoisomerase I inhibitors, in particular the antitumor agent camptothecin, trigger topoisomerase I-mediated DNA cleavage selectively in the proximity of the binding site of the oligonucleotide vector. In the present study, we have performed a systematic analy...

journal_title：Nucleic acids research

authors： Arimondo PB,Angenault S,Halby L,Boutorine A,Schmidt F,Monneret C,Garestier T,Sun JS,Bailly C,Hélène C

更新日期：2003-07-15 00:00:00

abstract：:Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the lack of efficient and accurate experimental and computational methods for their characterization, which has largely hindere...

journal_title：Nucleic acids research

authors： Zhang S,Xu M,Li S,Su Z

更新日期：2009-06-01 00:00:00