Abstract:
:CS23D (chemical shift to 3D structure) is a web server for rapidly generating accurate 3D protein structures using only assigned nuclear magnetic resonance (NMR) chemical shifts and sequence data as input. Unlike conventional NMR methods, CS23D requires no NOE and/or J-coupling data to perform its calculations. CS23D accepts chemical shift files in either SHIFTY or BMRB formats, and produces a set of PDB coordinates for the protein in about 10-15 min. CS23D uses a pipeline of several preexisting programs or servers to calculate the actual protein structure. Depending on the sequence similarity (or lack thereof) CS23D uses either (i) maximal subfragment assembly (a form of homology modeling), (ii) chemical shift threading or (iii) shift-aided de novo structure prediction (via Rosetta) followed by chemical shift refinement to generate and/or refine protein coordinates. Tests conducted on more than 100 proteins from the BioMagResBank indicate that CS23D converges (i.e. finds a solution) for >95% of protein queries. These chemical shift generated structures were found to be within 0.2-2.8 A RMSD of the NMR structure generated using conventional NOE-base NMR methods or conventional X-ray methods. The performance of CS23D is dependent on the completeness of the chemical shift assignments and the similarity of the query protein to known 3D folds. CS23D is accessible at http://www.cs23d.ca.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wishart DS,Arndt D,Berjanskii M,Tang P,Zhou J,Lin Gdoi
10.1093/nar/gkn305subject
Has Abstractpub_date
2008-07-01 00:00:00pages
W496-502issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkn305journal_volume
36pub_type
杂志文章abstract::The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling val...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.1.98
更新日期:2001-01-01 00:00:00
abstract::Recent studies show that the region of DNA brought into close proximity to the fetal gamma-globin genes in deletional forms of hereditary persistence of fetal hemoglobin (HPFH) is selectively hypomethylated (and presumably active) in normal erythroid tissue. This region is normally located approximately 100 kilobases ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.13.5169
更新日期:1987-07-10 00:00:00
abstract::Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic hybridization, SNP arrays and DNA sequencing platforms. Many techniques are available for detecting recurring aberrations across multiple tumor samples, including CMAR, STAC, GISTIC and KC-SMART...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt155
更新日期:2013-05-01 00:00:00
abstract::Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery. Many databases have been built to host and make available such data to the community, but these databases are frequently limited in scope and/or content. BioMuta, a database of cancer-associated si...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx907
更新日期:2018-01-04 00:00:00
abstract::DNA topoisomerase II (topo II) changes DNA topology by cleavage/re-ligation cycle(s) and thus contributes to various nuclear DNA transactions. It is largely unknown how the enzyme is controlled in a nuclear context. Several studies have suggested that its C-terminal domain (CTD), which is dispensable for basal relaxat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku640
更新日期:2014-08-01 00:00:00
abstract::Mitochondrial DNA from human tissue culture cells contains heterogeneous sequences located within a previously identified, evolutionarily conserved region termed CSB-2. CSB-2 is located near the origin of heavy-strand mitochondrial DNA synthesis and the major transcriptional promoters for each strand of human mitochon...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.22.8093
更新日期:1985-11-25 00:00:00
abstract::One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm093
更新日期:2007-01-01 00:00:00
abstract::(19)F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp862
更新日期:2009-12-01 00:00:00
abstract::Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt636
更新日期:2013-10-01 00:00:00
abstract::A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.1.57
更新日期:1986-01-10 00:00:00
abstract::As protein-protein interactions are crucial in most biological processes, it is valuable to understand how and where protein pairs interact. We developed a web server HOMCOS (Homology Modeling of Complex Structure, http://biunit.naist.jp/homcos) to predict interacting protein pairs and interacting sites by homology mo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn218
更新日期:2008-07-01 00:00:00
abstract::We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.18.3433
更新日期:2000-09-15 00:00:00
abstract::The helical twist of poly d(A-s4T) was determined from the periodicity of the cleavage patterns of the double stranded polydeoxynucleotide adsorbed on calcium phosphate and found to be 14 bp per turn. Both cleavage patterns and 31P NMR spectra indicate a mononucleotide structure rather than an alternating B DNA like p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.5.2241
更新日期:1986-03-11 00:00:00
abstract::Fibroblast growth factor receptor 3 (FGFR3) plays an important role in cartilage development. Although upregulation of FGFR3 expression in response to bone morphogenetic protein-2 (BMP-2) has been reported, the molecular mechanisms remain unknown. In this study, we used in vivo approaches to characterize BMP-2-induced...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp261
更新日期:2009-07-01 00:00:00
abstract::The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1022
更新日期:2021-01-08 00:00:00
abstract::Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt718
更新日期:2013-11-01 00:00:00
abstract::In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) ret...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm697
更新日期:2008-01-01 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::Cyclic AMP response element binding protein (CREB) activates transcription of cAMP response element (CRE)-containing promoters following an elevation of intracellular cAMP. Here we show that CREB and the highly related protein ATF-1 are also potent transcription inhibitors. Strikingly, CREB inhibits transcription of m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.12.2907
更新日期:1993-06-25 00:00:00
abstract::Protein classification by machine learning algorithms is now widely used in structural and functional annotation of proteins. The Protein Classification Benchmark collection (http://hydra.icgeb.trieste.it/benchmark) was created in order to provide standard datasets on which the performance of machine learning methods ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl812
更新日期:2007-01-01 00:00:00
abstract::A stable conformer of Escherichia coli tRNA(Glu), obtained in the absence of Mg(2+), is inactive in the aminoacylation reaction. Probing it with diethylpyrocarbonate, dimethyl sulfate and ribonuclease V1 revealed that it has a hairpin structure with two internal loops; the helical segments at both extremities have the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.17.3583
更新日期:1999-09-01 00:00:00
abstract::Double-stranded soybean leghemoglobin DNA was synthesized from leghemoglobin mRNA isolated from soybean nodules. The dsDNA was inserted into the Bam H1 site of plasmid pBR322 using the poly-dAT-joiner method. A cloned DNA fragment of one recombinant plasmid was isolated and characterized by restriction endonuclease di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.9.3061
更新日期:1979-07-11 00:00:00
abstract::The oncoprotein c-Myc plays an important role in cell proliferation, transformation, inhibition of differentiation and apoptosis. These functions most likely result from the transcription factor activity of c-Myc. As a heterodimer with Max, the c-Myc protein binds to the E-box sequence (CACGTG), which is also recogniz...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.8.1493
更新日期:1997-04-15 00:00:00
abstract::The antigene strategy based on site-specific recognition of duplex DNA by triplex DNA formation has been exploited in a wide range of biological activities. However, specific triplex formation is mostly restricted to homo-purine strands within the target duplex DNA, due to the destabilizing effect of CG and TA inversi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky704
更新日期:2018-09-28 00:00:00
abstract::To study the effect of intron size on splicing efficiency we have varied the size of the avian leukosis virus (ALV) env mRNA intron in a cloned ALV genome. This was accomplished by deletion of ALV sequences or insertion of phage lambda DNA. The effect of these modifications on splicing was analyzed by microinjection o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.19.6177
更新日期:1982-10-11 00:00:00
abstract::A mass spectral method is described for the detection and identification of unusual nucleotide residues present in DNAs. Analysis by this method of intact, underivatized DNA from salmon sperm, calf thymus, mouse L-cells, wheat germ, M. lysodeikticus, E. Coli, and the bacteriophages 0X-174, fd, and lamda, yields diagno...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.11.2959
更新日期:1976-11-01 00:00:00
abstract::Non-coding RNAs (ncRNAs) have diverse essential biological functions in all organisms, and in eukaryotes, two such classes of ncRNAs are the small nucleolar (sno) and small nuclear (sn) RNAs. In this study, we have identified and characterized a collection of sno and snRNAs in Giardia lamblia, by exploiting our discov...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks887
更新日期:2012-11-01 00:00:00
abstract::Overexpressed in colon carcinoma-1 (OCC-1) is one of the earliest annotated long noncoding RNAs (lncRNAs) in colorectal cancer (CRC); however, its function remains largely unknown. Here, we revealed that OCC-1 plays a tumor suppressive role in CRC. OCC-1 knockdown by RNA interference promotes cell growth both in vitro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky214
更新日期:2018-06-20 00:00:00
abstract::We describe a new exonuclease-based method for joining and/or constructing two or more DNA molecules. DNA fragments containing ends complementary to those of a vector or another independent molecules were generated by the polymerase chain reaction. The 3' ends of these molecules as well as the vector DNA were then rec...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.8.1889
更新日期:1993-04-25 00:00:00
abstract::We determined the structure around the gap region between 28S alpha and 28S beta rRNA of Bombyx mori, a lepidopteran insect, to know the introduction mechanism of the hidden break, an interruption of the phosphodiester bond specific to the 28S rRNA of protostomes. Sequence analysis and S1 nuclease mapping suggested th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.16.6393
更新日期:1986-08-26 00:00:00