DynOmics: dynamics of structural proteome and beyond.


:DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core of the portal is a newly developed server, ENM 1.0, which permits users to efficiently generate information on the collective dynamics of any structure in PDB format, user-uploaded or database-retrieved. ENM 1.0 integrates two widely used elastic network models (ENMs)-the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM), extended to take account of molecular environment. It enables users to assess potentially functional sites, signal transduction or allosteric communication mechanisms, and protein-protein and protein-DNA interaction poses, in addition to delivering ensembles of accessible conformers reconstructed at atomic details based on the global modes of motions predicted by the ANM. The 'environment' is defined in a flexible manner, from lipid bilayer and crystal contacts, to substrate or ligands bound to a protein, or surrounding subunits in a multimeric structure or assembly. User-friendly interactive features permit users to easily visualize how the environment alter the intrinsic dynamics of the query systems. ENM 1.0 can be accessed at http://enm.pitt.edu/ or http://dyn.life.nthu.edu.tw/oENM/.


Nucleic Acids Res


Nucleic acids research


Li H,Chang YY,Lee JY,Bahar I,Yang LW




Has Abstract


2017-07-03 00:00:00














  • Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V.

    abstract::Oxanine (O) is a deamination product derived from guanine with the nitrogen at the N1 position substituted by oxygen. Cytosine, thymine, adenine, guanine as well as oxanine itself can be incorporated by Klenow Fragment to pair with oxanine in a DNA template with similar efficiency, indicating that oxanine in DNA may c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hitchcock TM,Gao H,Cao W

    更新日期:2004-08-02 00:00:00

  • Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome.

    abstract::Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when experimental, restricted to small datasets; particularly poor attention has been given to genes with low CUB. In this work, co...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: dos Reis M,Wernisch L,Savva R

    更新日期:2003-12-01 00:00:00

  • The 'endo-blue method' for direct cloning of restriction endonuclease genes in E. coli.

    abstract::A new E. coli strain has been constructed that contains the dinD1::LacZ+ fusion and is deficient in methylation-dependent restriction systems (McrA-, McrBC-, Mrr-). This strain has been used to clone restriction endonuclease genes directly into E. coli. When E. coli cells are not fully protected by the cognate methyla...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fomenkov A,Xiao JP,Dila D,Raleigh E,Xu SY

    更新日期:1994-06-25 00:00:00

  • Methylation of nucleosomal and nuclease sensitive DNA.

    abstract::The proportion of cytosines methylated in the DNA of nucleosome oligomers and of core particles appears indistinguishable from that of total nuclear DNA from CHO cells. However the DNA in nucleoprotein which is initially released from nuclei by treatment with very low levels of micrococcal nuclease and the first 10% o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Adams RL,McKay EL,Douglas JT,Burdon RH

    更新日期:1977-09-01 00:00:00

  • Oxidative damage to 5-methylcytosine in DNA.

    abstract::Exposure of pyrimidines of DNA to ionizing radiation under aerobic conditions or oxidizing agents results in attack on the 5,6 double bond of the pyrimidine ring or on the exocyclic 5-methyl group. The primary product of oxidation of the 5,6 double bond of thymine is thymine glycol, while oxidation of the 5-methyl gro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zuo S,Boorstein RJ,Teebor GW

    更新日期:1995-08-25 00:00:00

  • MGView: an alignment and visualization tool to enhance gap closure of microbial genomes.

    abstract::Gap closure is a challenging phase in microbial random shotgun genome sequencing projects, particularly since genome assemblies are often complicated by the presence of repeat elements, insertion sequences and other similar factors that contribute to sequence misassemblies. While it is well recognized that the conserv...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Herron-Olson L,Freeman J,Zhang Q,Retzel EF,Kapur V

    更新日期:2003-09-01 00:00:00

  • PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

    abstract::The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific ge...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Urban M,Cuzick A,Rutherford K,Irvine A,Pedro H,Pant R,Sadanadan V,Khamari L,Billal S,Mohanty S,Hammond-Kosack KE

    更新日期:2017-01-04 00:00:00

  • hnRNP A2, a potential ssDNA/RNA molecular adapter at the telomere.

    abstract::The heterogeneous nuclear ribonucleoprotein (hnRNP) A2 is a multi-tasking protein that acts in the cytoplasm and nucleus. We have explored the possibility that this protein is associated with telomeres and participates in their maintenance. Rat brain hnRNP A2 was shown to have two nucleic acid binding sites. In the pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Moran-Jones K,Wayman L,Kennedy DD,Reddel RR,Sara S,Snee MJ,Smith R

    更新日期:2005-01-19 00:00:00

  • DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization.

    abstract::Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gilson E,Perrin D,Hofnung M

    更新日期:1990-07-11 00:00:00

  • Accurate and efficient N-6-adenosine methylation in spliceosomal U6 small nuclear RNA by HeLa cell extract in vitro.

    abstract::Human U6 small nuclear RNA (U6 snRNA), an abundant snRNA required for splicing of pre-mRNAs, contains several post-transcriptional modifications including a single m6A (N-6-methyladenosine) at position 43. This A-43 residue is critical for the function of U6 snRNA in splicing of pre-mRNAs. Yeast and plant U6 snRNAs al...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shimba S,Bokar JA,Rottman F,Reddy R

    更新日期:1995-07-11 00:00:00

  • ZAR1 and ZAR2 are required for oocyte meiotic maturation by regulating the maternal transcriptome and mRNA translational activation.

    abstract::Zar1 was one of the earliest mammalian maternal-effect genes to be identified. Embryos derived from Zar1-null female mice are blocked before zygotic genome activation; however, the underlying mechanism remains unclear. By knocking out Zar1 and its homolog Zar2 in mice, we revealed a novel function of these genes in oo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rong Y,Ji SY,Zhu YZ,Wu YW,Shen L,Fan HY

    更新日期:2019-12-02 00:00:00

  • Characterization of hybridization between synthetic oligodeoxynucleotides and RNA in living cells.

    abstract::Cells internalized synthetic oligonucleotides (oligos) in culture. The hybridization of these molecules to target RNA in the living cell was subsequently detected and characterized after fixation of the cells, with or without previous detergent extraction. Hybridized oligo was distinguished from free oligo in the cell...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Politz JC,Taneja KL,Singer RH

    更新日期:1995-12-25 00:00:00

  • Blotting of RNA onto ion exchange paper allowing subsequent characterization by in situ translation in addition to blot hybridization.

    abstract::We present the preparation of an ion exchange paper which can be used as a solid carrier in the transfer of RNA from gels. In addition to detection by blot hybridization to specific probes, transferred RNA can be characterized by cell-free translation in situ. Preparation of the paper is simple, inexpensive and reprod...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Saris CJ,Franssen HJ,Heuyerjans JH,van Eenbergen J,Bloemers HP

    更新日期:1982-08-25 00:00:00

  • Release of promoter-proximal paused Pol II in response to histone deacetylase inhibition.

    abstract::A correlation between histone acetylation and transcription has been noted for a long time, but little is known about what step(s) in the transcription cycle is influenced by acetylation. We have examined the immediate transcriptional response to histone deacetylase (HDAC) inhibition, and find that release of promoter...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vaid R,Wen J,Mannervik M

    更新日期:2020-05-21 00:00:00

  • SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences.

    abstract::The single nucleotide polymorphisms (SNPs) in conserved protein regions have been thought to be strong candidates that alter protein functions. Thus, we have developed SNP@Domain, a web resource, to identify SNPs within human protein domains. We annotated SNPs from dbSNP with protein structure-based as well as sequenc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Han A,Kang HJ,Cho Y,Lee S,Kim YJ,Gong S

    更新日期:2006-07-01 00:00:00

  • Purification, characterization and molecular cloning of TGP1, a novel G-DNA binding protein from Tetrahymena thermophila.

    abstract::G-DNA, a polymorphic family of four-stranded DNA structures, has been proposed to play roles in a variety of biological processes including telomere function, meiotic recombination and gene regulation. Here we report the purification and cloning of TGP1, a G-DNA specific binding protein from Tetrahymena thermophila. T...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lu Q,Schierer T,Kang SG,Henderson E

    更新日期:1998-04-01 00:00:00

  • Conditional degradation of SDE2 by the Arg/N-End rule pathway regulates stress response at replication forks.

    abstract::Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rageul J,Park JJ,Jo U,Weinheimer AS,Vu TTM,Kim H

    更新日期:2019-05-07 00:00:00

  • Activation of RuvC Holliday junction resolvase in vitro.

    abstract::The Escherichia coli RuvC protein is an endonuclease that resolves Holliday junctions. In vitro, the protein shows efficient structure-specific binding of Holliday junctions, yet the rate of junction resolution is remarkably low. We have mapped the sites of cleavage on a synthetic junction through which a crossover ca...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shah R,Bennett RJ,West SC

    更新日期:1994-07-11 00:00:00

  • The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse.

    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


    authors: Blake JA,Bult CJ,Eppig JT,Kadin JA,Richardson JE,Mouse Genome Database Group.

    更新日期:2014-01-01 00:00:00

  • Characterization of the unique intron-exon junctions of Euglena gene(s) encoding the polyprotein precursor to the light-harvesting chlorophyll a/b binding protein of photosystem II.

    abstract::The precursor to the Euglena light harvesting chlorophyll a/b binding protein of photosystem II (LHCPII) is a polyprotein containing multiple copies of LHCPII covalently joined by a decapeptide linker. cDNA and genomic clones encoding the 5' and 3' end of a 6.6 kb LHCPII mRNA were sequenced. A 3.1 kb genomic region en...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Muchhal US,Schwartzbach SD

    更新日期:1994-12-25 00:00:00

  • Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells.

    abstract::Targeted modulation of gene expression represents a valuable approach to understand the mechanisms governing gene regulation. In a therapeutic context, it can be exploited to selectively modify the aberrant expression of a disease-causing gene or to provide the target cells with a new function. Here, we have establish...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mlambo T,Nitsch S,Hildenbeutel M,Romito M,Müller M,Bossen C,Diederichs S,Cornu TI,Cathomen T,Mussolino C

    更新日期:2018-05-18 00:00:00

  • Selective isolation and detailed analysis of intra-RNA cross-links induced in the large ribosomal subunit of E. coli: a model for the tertiary structure of the tRNA binding domain in 23S RNA.

    abstract::Intramolecular RNA cross-links were induced within the large ribosomal subunit of E. coli by mild ultraviolet irradiation. Regions of the 23S RNA previously implicated in interactions with ribosomal-bound tRNA were then specifically excised by addressed cleavage using ribonuclease H, in conjunction with synthetic comp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mitchell P,Osswald M,Schueler D,Brimacombe R

    更新日期:1990-08-11 00:00:00

  • Dynamic changes in intron retention are tightly associated with regulation of splicing factors and proliferative activity during B-cell development.

    abstract::Intron retention (IR) has been proposed to modulate the delay between transcription and translation. Here, we provide an exhaustive characterization of IR in differentiated white blood cells from both the myeloid and lymphoid lineage where we observed highest levels of IR in monocytes and B-cells, in addition to previ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ullrich S,Guigó R

    更新日期:2020-02-20 00:00:00

  • Quantitation of supercoiled circular content in plasmid DNA solutions using a fluorescence-based method.

    abstract::A method for quantifying the proportion of supercoiled circular (SC) forms in DNA solutions is described. The method (SCFluo) takes advantage of the reversible denaturation property of SC forms and the high specificity of the PicoGreen fluorochrome for double-stranded (ds)DNA. Fluorescence values of forms capable of r...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Levy MS,Lotfian P,O'Kennedy R,Lo-Yim MY,Shamlou PA

    更新日期:2000-06-15 00:00:00

  • Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing.

    abstract::A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variant...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wang W,Shen P,Thiyagarajan S,Lin S,Palm C,Horvath R,Klopstock T,Cutler D,Pique L,Schrijver I,Davis RW,Mindrinos M,Speed TP,Scharfe C

    更新日期:2011-01-01 00:00:00

  • Linker phosphoramidite reagents for the attachment of the first nucleoside to underivatized solid-phase supports.

    abstract::New linker phosphoramidite reagents containing a cleavable 3'-ester linkage are used for attaching the first nucleoside to the surface of a solid- phase support. Inexpensive, underivatized amino supports, such as long chain alkylamine controlled-pore glass, can serve as universal supports. No modifications to phosphor...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pon RT,Yu S

    更新日期:2004-01-29 00:00:00

  • Analysis of microRNA signatures using size-coded ligation-mediated PCR.

    abstract::The expression pattern and regulatory functions of microRNAs (miRNAs) are intensively investigated in various tissues, cell types and disorders. Differential miRNA expression signatures have been revealed in healthy and unhealthy tissues using high-throughput profiling methods. For further analyses of miRNA signatures...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Arefian E,Kiani J,Soleimani M,Shariati SA,Aghaee-Bakhtiari SH,Atashi A,Gheisari Y,Ahmadbeigi N,Banaei-Moghaddam AM,Naderi M,Namvarasl N,Good L,Faridani OR

    更新日期:2011-07-01 00:00:00

  • Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 with improved proof-reading enhances homology-directed repair.

    abstract::Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) predominantly induces non-homologous end joining (NHEJ), which generates random insertions or deletions, whereas homology-directed repair (HDR), which generates precise recombination products, is ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kato-Inui T,Takahashi G,Hsu S,Miyaoka Y

    更新日期:2018-05-18 00:00:00

  • RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.

    abstract::In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centri...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Uyar B,Yusuf D,Wurmus R,Rajewsky N,Ohler U,Akalin A

    更新日期:2017-06-02 00:00:00

  • Long W tracts are over-represented in the Escherichia coli and Haemophilus influenzae genomes.

    abstract::The occurrence of DNA tracts of the three binary base combinations: R.Y, K.M and W;S has been mapped in the complete genomes of Haemophilus influenzae and Escherichia coli. A highly significant over-representation of W tracts is observed in both bacteria. The excess of W tracts is particularly striking in the 10% inte...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shomer B,Yagil G

    更新日期:1999-11-15 00:00:00