Abstract:
:We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium, allowing collaborative structural proteomics to be carried out in a distributed fashion. The core of SPINE is a laboratory information management system (LIMS) for key bits of information related to the progress of the consortium in cloning, expressing and purifying proteins and then solving their structures by NMR or X-ray crystallography. Originally, SPINE focused on tracking constructs, but, in its current form, it is able to track target sample tubes and store detailed sample histories. The core database comprises a set of standard relational tables and a data dictionary that form an initial ontology for proteomic properties and provide a framework for large-scale data mining. Moreover, SPINE sits at the center of a federation of interoperable information resources. These can be divided into (i) local resources closely coupled with SPINE that enable it to handle less standardized information (e.g. integrated mailing and publication lists), (ii) other information resources in the NESG consortium that are inter-linked with SPINE (e.g. crystallization LIMS local to particular laboratories) and (iii) international archival resources that SPINE links to and passes on information to (e.g. TargetDB at the PDB).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Goh CS,Lan N,Echols N,Douglas SM,Milburn D,Bertone P,Xiao R,Ma LC,Zheng D,Wunderlich Z,Acton T,Montelione GT,Gerstein Mdoi
10.1093/nar/gkg397keywords:
subject
Has Abstractpub_date
2003-06-01 00:00:00pages
2833-8issue
11eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::Calf thymus nucleosomes exhibit two different and independent hydrodynamic responses to diminishing salt concentration. One change is gradual over the range 40 to 0.2 mM Na+ and is accompanied by decreases in contact-site cross-linking efficiency. The other change is abrupt, being centered between 1 and 2 mM Na+. We f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.21.4969
更新日期:1980-11-11 00:00:00
abstract::A growing body of evidence suggests that genes transcribed by RNA polymerase III exhibit multiple functions within a chromosome. While the predominant function of these genes is the synthesis of RNA molecules, certain RNA polymerase III genes also function as genomic landmarks. Transfer RNA genes are known to exhibit ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh858
更新日期:2004-09-30 00:00:00
abstract::We have sequenced the external transcribed spacer (ETS) of a ribosomal transcription unit from Xenopus laevis, together with sections of the preceding non-transcribed spacer. Our analysis was carried out on the same cloned transcription unit as that from which the internal transcribed spacers (ITS) were previously seq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.7.2387
更新日期:1982-04-10 00:00:00
abstract::Advancement in the field of computational research has made it possible for the in silico methods to offer significant benefits to both regulatory needs and requirements for risk assessments, and pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox-II that incorporates molecular ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky318
更新日期:2018-07-02 00:00:00
abstract::The polypeptides recognized by a monoclonal antibody against calf thymus DNA polymerase alpha (secreted from a hybridoma CL22 -2- 42B , Nucleic Acids Res. (1982) 10, 4703-4713) were identified by the immunoblot method as the large polypeptides of the partially-purified 10S DNA polymerase alpha fraction. Using an immun...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.11.4455
更新日期:1984-06-11 00:00:00
abstract::Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG(5)T, in ammonium acetate. The intermediates and products were separated according to their mass (number of strands and inner cations) and quantified. The study of the temporal ev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq208
更新日期:2010-08-01 00:00:00
abstract::The role of the cyclic-AMP (cAMP) responsive element (CRE) in eukaryotic gene transcription was investigated in several cell lines transfected by constructs containing the chloramphenicol acetyltransferase (CAT) gene linked to the three different promoters, simian virus (SV) 40, human c-Ha-ras-1, or chicken beta-actin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.4.1521
更新日期:1989-02-25 00:00:00
abstract::In eukaryotes, exposure to stress conditions causes a shift from cap-dependent to cap-independent translation. In trypanosomatids, environmental switches are the driving force of a developmental program of gene expression, but it is yet unclear how their translation machinery copes with their constantly changing envir...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr555
更新日期:2011-10-01 00:00:00
abstract::The chromatin-remodelling complex B-WICH, comprised of William syndrome transcription factor, the ATPase SNF2h and nuclear myosin, specifically activates RNA polymerase III transcription of the 5S rRNA and 7SL genes. However, the underlying mechanism is unknown. Using high-resolution MN walking we demonstrate here tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv312
更新日期:2015-05-19 00:00:00
abstract::Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell M...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky152
更新日期:2018-05-18 00:00:00
abstract::ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release comprises 30 145 records curated from 922 publications and describing regul...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm967
更新日期:2008-01-01 00:00:00
abstract::In the fission yeast Schizosaccharomyces pombe, the cdc11 gene is required for the initiation of septum formation at the end of mitosis. The sce3 gene was cloned as a multi-copy suppressor of the heat-sensitive mutant cdc11-136. When over-expressed, it rescues all mutants of cdc11 and also a heat-sensitive allele of c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.17.3433
更新日期:1997-09-01 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::NONO, SFPQ and PSPC1 make up a family of proteins with diverse roles in transcription, RNA processing and DNA double-strand break (DSB) repair. To understand long-term effects of loss of NONO, we characterized murine embryonic fibroblasts (MEFs) from knockout mice. In the absence of genotoxic stress, wild-type and mut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku650
更新日期:2014-09-01 00:00:00
abstract::We used 2D protein gel electrophoresis and DNA microarray technologies to systematically analyze genes under glucose repression in B:acillus subtilis. In particular, we focused on genes expressed after the shift from glycolytic to gluconeogenic at the middle logarithmic phase of growth in a nutrient sporulation medium...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.3.683
更新日期:2001-02-01 00:00:00
abstract::The binding of anti poly(I). poly (C) Fab fragments to double or triple stranded polynucletides has been studied by fluorescence. Association constants were deduced from competition experiments. The comparison of the association constants leads to the conclusion that several atoms of the base residues do not interact ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.12.3337
更新日期:1976-12-01 00:00:00
abstract::According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer-promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw371
更新日期:2016-09-06 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::Homologous recombination (HR) is important in repairing errors of replication and other forms of DNA damage. In mammalian cells, potential templates include the homologous chromosome, and after DNA replication, the sister chromatid. Previous work has shown that the mammalian recombination machinery is organized to sup...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh280
更新日期:2004-02-20 00:00:00
abstract::In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1133
更新日期:2015-12-02 00:00:00
abstract::CeR-2 RNA is one of the newly identified Caenorhabditis elegans noncoding RNAs (ncRNAs). The characterization of CeR-2 by RNomic studies has failed to classify it into any known ncRNA family. In this study, we examined the spatiotemporal expression patterns of CeR-2 to gain insight into its function. CeR-2 is expresse...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq335
更新日期:2010-09-01 00:00:00
abstract::The tight-binding I12-X86 lac repressor binds to non-operator DNA in a sequence-specific fashion. Using the DNA of the E. coli I gene we have investigated these sequence-specific interactions and compared them to the operator binding of wild-type repressor. The specific, non-operator DNA interactions are sensitive to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.3.487
更新日期:1980-02-11 00:00:00
abstract::We have examined the replication patterns of ribosomal DNA plasmids in vivo and in vitro using Xenopus eggs. Plasmids carrying different parts of the Xenopus ribosomal DNA sequence were allowed to replicate either in vitro in an egg extract or in vivo after microinjection into unfertilized eggs. The replication interm...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.7.1463
更新日期:1992-04-11 00:00:00
abstract::Interactions between proteins, drugs, water and B-DNA minor groove have been analyzed in crystal structures of 60 protein-DNA and 14 drug-DNA complexes. It was found that only purine N3, pyrimidine O2, guanine N2 and deoxyribose O4' are involved in the interactions, and that contacts to N3 and O2 are most frequent and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.5.1182
更新日期:2002-03-01 00:00:00
abstract::Thyroglobulin (Tg), the precursor of thyroid hormones, is a 660.000 Da dimeric glycoprotein synthesized exclusively in the thyroid gland. We have cloned the human thyroglobulin gene from cosmid and phage libraries and constructed a complete restriction map. The gene encodes an 8.7 kb mRNA, covers at least 300 kb DNA a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.13.5171
更新日期:1986-07-11 00:00:00
abstract:T:Activator protein 1 (AP-1) is a transcription factor that recognizes two versions of a 7-base pair response element, either 5΄- GAG CA-3΄ or 5΄- GAG CA-3΄ (where M = 5-methylcytosine). These two elements share the feature that 5-methylcytosine and thymine both have a methyl group in the same position, 5-carbon of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx057
更新日期:2017-03-17 00:00:00
abstract::The pyrrole-imidazole (Py-Im) triamide-cyclopropa pyrroloindole (CPI) conjugates ImPyImLDu86 (7) and ImImPyLDu86 (14) were synthesized and their alkylating activities and inhibitory effects on DNA hydrolysis by restriction endonucleases were examined. Sequencing gel analysis demonstrated that conjugates 7 and 14 speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf486
更新日期:2002-09-01 00:00:00
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
doi:10.1093/nar/27.22.4491
更新日期:1999-11-15 00:00:00
abstract::In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. Ther...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh367
更新日期:2004-07-01 00:00:00
abstract::The 0.048502 megabase (Mb), primarily double-stranded DNA of bacteriophage lambda has single-stranded, complementary termini (cohesive ends) that undergo either spontaneous intramolecular joining to form open circular DNA or spontaneous intermolecular joining to form linear, end-to-end oligomeric DNAs (concatemers); c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.11.3047
更新日期:1991-06-11 00:00:00