Abstract：
:We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at least some structural information. At present it contains >120 motions, most of which are of proteins. Protein motions are further classified hierarchically into a limited number of categories, first on the basis of size (distinguishing between fragment, domain and subunit motions) and then on the basis of packing. Our packing classification divides motions into various categories (shear, hinge, other) depending on whether or not they involve sliding over a continuously maintained and tightly packed interface. In addition, the database provides some indication about the evidence behind each motion (i.e. the type of experimental information or whether the motion is inferred based on structural similarity) and attempts to describe many aspects of a motion in terms of a standardized nomenclature (e.g. the maximum rotation, the residue selection of a fixed core, etc.). Currently, we use a standard relational design to implement the database. However, the complexity and heterogeneity of the information kept in the database makes it an ideal application for an object-relational approach, and we are moving it in this direction. Specifically, in terms of storing complex information, the database contains plausible representations for motion pathways, derived from restrained 3D interpolation between known endpoint conformations. These pathways can be viewed in a variety of movie formats, and the database is associated with a server that can automatically generate these movies from submitted coordinates.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gerstein M,Krebs Wdoi
10.1093/nar/26.18.4280subject
Has Abstractpub_date
1998-09-15 00:00:00pages
4280-90issue
18eissn
0305-1048issn
1362-4962pii
gkb684journal_volume
26pub_type
杂志文章abstract：:Arabidopsis thaliana is a reference plant that has been studied intensively for several decades. Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount of data from A. thaliana, which has facilitated data-driven approaches to unravel the genetic organization o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1053
更新日期：2015-01-01 00:00:00
abstract：:A new method is described for the direct construction of randomly mutagenized genes by applying the polymerase chain reaction (PCR) to an oligonucleotide synthesized using doped nucleotide reservoirs. We have demonstrated the utility of this method by generating a library of mutant HIV-1 tat genes. Several arbitrarily...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.20.5311
更新日期：1992-10-25 00:00:00
abstract：:The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.5.667
更新日期：1975-05-01 00:00:00
abstract：:The molecular mechanism in pancreatic β cells underlying hyperlipidemia and insulin insufficiency remains unclear. Here, we find that the fatty acid-induced decrease in insulin levels occurs due to a decrease in insulin translation. Since regulation at the translational level is generally mediated through RNA-binding ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky867
更新日期：2018-12-14 00:00:00
abstract：:Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks. Hundreds of sRNAs have been discovered by genome-wide screens and most of these sRNAs exert their functions by base-pairing with target mRNAs. However, studies addressing the molecul...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky765
更新日期：2018-11-16 00:00:00
abstract：:The TransTerm database of termination codon contexts has been extended to include sense codon usage, and initiation codon contexts. The database was constructed from 23,721 coding sequences from 93 organisms. The database contains: a) the sequence around the termination codon (-10, +10); b) the sequence around the ini...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.17.3620
更新日期：1994-09-01 00:00:00
abstract：:Protein-RNA interactions in small nuclear ribonucleoproteins (UsnRNPs) from HeLa cells were investigated by irradiation of purified nucleoplasmic snRNPs U1 to U6 with UV light at 254 nm. The cross-linked proteins were analyzed on one- and two-dimensional gel electrophoresis systems, and the existence of a stable cross...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.23.10985
更新日期：1988-12-09 00:00:00
abstract：:This laboratory has established in previous studies that Pmel 17, a gene expressed specifically in melanocytes, maps near the silver coat color locus (si/si) on mouse chromosome 10. In the current study, we have focused on determining whether or not the si allele carries a mutation in Pmel 17. Pmel 17 cDNA clones, iso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.1.154
更新日期：1995-01-11 00:00:00
abstract：:siRNAs confer sequence specific and robust silencing of mRNA. By virtue of these properties, siRNAs have become therapeutic candidates for disease intervention. However, their use as therapeutic agents can be hampered by unintended off-target effects by either or both strands of the siRNA duplex. We report here that u...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq961
更新日期：2011-03-01 00:00:00
abstract：:The mitochondrial DNA of Neurospora crassa has a heterogeneous intramolecular base distribution. A contiguous piece, representing at least 30% of the total genome, has a G+C content that is 6% lower than the overall G+C content of the DNA. The genes for both ribosomal RNAs are contained in the remaining, relatively G+...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.1.129
更新日期：1977-01-01 00:00:00
abstract：:Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt961
更新日期：2014-01-01 00:00:00
abstract：:CENP-A and CENP-B are major components of centromeric chromatin. CENP-A is the histone H3 variant, which forms the centromere-specific nucleosome. CENP-B specifically binds to the CENP-B box DNA sequence on the centromere-specific repetitive DNA. In the present study, we found that the CENP-A nucleosome more stably re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv405
更新日期：2015-05-26 00:00:00
abstract：:Electron microscopic technique was used to examine the structures of SV40 DNA recombination intermediates induced by ultraviolet irradiation as an approach for understanding recombination mechanisms in animal cells. Putative recombination intermediate with the characteristic Holliday junction was observed in both SV40...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.25.7193
更新日期：1991-12-01 00:00:00
abstract：:Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp468
更新日期：2009-08-01 00:00:00
abstract：:The noncoding RNA database (ncRNAdb) was created as a source of information on RNA molecules, which do not possess protein-coding capacity. It is now widely accepted that, in addition to constitutively expressed, housekeeping or infrastructural RNAs, there is a wide variety of RNAs participating in mechanisms involved...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl994
更新日期：2007-01-01 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
pub_type： 杂志文章
doi：10.1093/nar/10.24.8031
更新日期：1982-12-20 00:00:00
abstract：:PAHdb (http://www.mcgill.ca/pahdb ) is a curated relational database (Fig. 1) of nucleotide variation in the human PAH cDNA (GenBank U49897). Among 328 different mutations by state (Fig. 2) the majority are rare mutations causing hyperphenylalaninemia (HPA) (OMIM 261600), the remainder are polymorphic variants without...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.220
更新日期：1998-01-01 00:00:00
abstract：:We have used DNase I footprinting to examine the association kinetics of GA-, GT- and CT-containing oligonucleotides with the target sequence (GGA)5GG. (CCT)5CC. These reactions are slow yielding bimolecular association rate constants between 50 and 2000 M-1s-1. We find that GT-containing oligonucleotides bind much fa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.16.3269
更新日期：1997-08-15 00:00:00
abstract：:Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the exploration and comparative study of domain architectures in both proteins and genes. The current release of SMART contains ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn808
更新日期：2009-01-01 00:00:00
abstract：:E. coli C6 rel- met- cys- was cultured in a fully supplemented medium and in media lacking cysteine or methionine. tRNA isolated from the three cultures containted, respectively, a normal complement of modified nucleosides; a deficiency in thiolated nucleosides and a deficiency in methylated nucleosides. Both sulfur-d...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.5.691
更新日期：1975-05-01 00:00:00
abstract：:A reporter assay was developed to detect and quantify nonsense codon suppression by chemically aminoacylated tRNAs in mammalian cells. It is based on the cellular expression of the enhanced green fluorescent protein (EGFP) as a reporter for the site-specific amino acid incorporation in its sequence using an orthogonal...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf128
更新日期：2002-12-01 00:00:00
abstract：:Heptadecaoligodeoxyribonucleotides containing one or more of the bases, 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (P), 2-amino-6-methoxyaminopurine (K), and hypoxanthine (I) and combinations of P with K and I have been synthesised on a DNA synthesiser. The stability of duplexes containing these basemodified ol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.19.5149
更新日期：1992-10-11 00:00:00
abstract：:Nucleotide incorporation opposite an oxidative form of adenine, 2-hydroxyadenine (2-OH-Ade) was investigated. When a primed template with 2-OH-Ade was treated with an exonuclease-deficient Klenow fragment of Escherichia coli DNA polymerase I (KFexo-), recombinant rat DNA polymerase beta (pol beta) or calf thymus DNA p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.5.761
更新日期：1995-03-11 00:00:00
abstract：:Foldback DNA, prepared from mouse and Scilla sibirica main band DNA, and from rye (Secale cereale) total DNA, was characterised by denaturation, renaturation, and electron microscopy. 3H-cRNA of this DNA was hybridised in situ to nuclei and chromosomes of the respective species. There is no universal labelling pattern...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.10.3589
更新日期：1978-10-01 00:00:00
abstract：:The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1013
更新日期：2020-12-16 00:00:00
abstract：:Trinucleotide repeat (TNR) expansions cause at least 17 heritable neurological diseases, including Huntington's disease. Expansions are thought to arise from abnormal processing of TNR DNA by specific trans-acting proteins. For example, the DNA repair complex MutSβ (MSH2-MSH3 heterodimer) is required in mice for on-go...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks810
更新日期：2012-11-01 00:00:00
abstract：:Small regulatory RNAs (sRNAs) from bacterial chromosomes became the focus of research over the past five years. However, relatively little is known in terms of structural requirements, kinetics of interaction with their targets and degradation in contrast to well-studied plasmid-encoded antisense RNAs. Here, we presen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm439
更新日期：2007-01-01 00:00:00
abstract：:Little is known about the regulation of the DNA damage-mediated gene expression in archaea. Here we report that the addition of actinomycin D to Sulfolobus solfataricus cultures triggers the expression of the radA paralogue sso0777. Furthermore, a specific retarded band is observed when electrophoretic mobility shift ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm782
更新日期：2007-01-01 00:00:00
abstract：:Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm979
更新日期：2008-01-01 00:00:00
abstract：:Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centre of the ribosome. Here, we present the 2.2 A crystal structure of tr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn922
更新日期：2009-02-01 00:00:00
