Abstract:
:MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Davis IW,Leaver-Fay A,Chen VB,Block JN,Kapral GJ,Wang X,Murray LW,Arendall WB 3rd,Snoeyink J,Richardson JS,Richardson DCdoi
10.1093/nar/gkm216subject
Has Abstractpub_date
2007-07-01 00:00:00pages
W375-83issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkm216journal_volume
35pub_type
杂志文章abstract::Human ADAR3 is a catalytically inactive member of the Adenosine Deaminase Acting on RNA (ADAR) protein family, whose active members catalyze A-to-I RNA editing in metazoans. Until now, the reasons for the catalytic incapability of ADAR3 has not been defined and its biological function rarely explored. Yet, its exclusi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz815
更新日期:2019-11-18 00:00:00
abstract::The genomic distribution of 23 nuclear genes from three dicotyledons (pea, sunflower, tobacco) and five monocotyledons of the Gramineae family (barley, maize, rice, oat, wheat) was studied by localizing these genes in DNA fractions obtained by preparative centrifugation in Cs2SO4/BAMD density gradients. Each one of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.7.1859
更新日期:1990-04-11 00:00:00
abstract::The solubility of adult beta-globin chromatin (beta A chromatin) from immature chicken red blood cells can be controlled by the presence or absence of n-butyrate in a cell incubation medium. In the absence of n-butyrate, only a small percentage (approximately 4%) of the total beta A chromatin is in a soluble chromatin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.6.1977
更新日期:1985-03-25 00:00:00
abstract::A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1055
更新日期:2016-01-08 00:00:00
abstract::DNA primer sets, labeled with two fluorescent dyes to exploit fluorescence energy transfer (ET), can be efficiently excited with a single laser line and emit strong fluorescence at distinctive wavelengths. Such ET primers are superior to single fluorophore-labeled primers for DNA sequencing and other multiple color-ba...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.6.1144
更新日期:1996-03-15 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::The mouse is widely used as system to study human genetic mechanisms. However, extensive rewiring of transcriptional regulatory networks often confounds translation of findings between human and mouse. Site-specific gain and loss of individual transcription factor binding sites (TFBS) has caused functional divergence ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky018
更新日期:2018-02-28 00:00:00
abstract::It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq399
更新日期:2010-07-01 00:00:00
abstract::High affinity antisense oligonucleotides (ASOs) containing bicylic modifications (BNA) such as locked nucleic acid (LNA) designed to induce target RNA cleavage have been shown to have enhanced potency along with a higher propensity to cause hepatotoxicity. In order to understand the mechanism of this hepatotoxicity, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1210
更新日期:2016-03-18 00:00:00
abstract::Proteins interacting with pre-mRNAs during early stages of spliceosome formation in a HeLa nuclear extract were investigated by photochemical RNA-protein crosslinking. The level of protein crosslinking to a beta-globin pre-mRNA was positively correlated with the presence of an intron. Proteins of 110,000, 59,000 and 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.11.3307
更新日期:1990-06-11 00:00:00
abstract::Mutations in the RecQ DNA helicase gene BLM give rise to Bloom's syndrome, which is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition. BLM helicase is highly active in binding and unwinding G-quadruplexes (G4s), which are physiological targets for BLM, as revealed by ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv361
更新日期:2015-05-19 00:00:00
abstract::SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm407
更新日期:2007-07-01 00:00:00
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
doi:10.1093/nar/gkq750
更新日期:2011-01-01 00:00:00
abstract::The lambdagt clones containing fragments of the Drosophila melanogaster genome were prepared and characterized by hybridization of their DNA with (I) lambdagt-cRNA; (2) lambdaC-cRNA; (3) Dm-cRNA; (4) the mRNA of D.melanogaster culture cells and (5) the stable cytoplasmic poly (A) RNA from the same source. The techniqu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.8.2115
更新日期:1976-08-01 00:00:00
abstract::Oligonucleotides synthesized in array format suffer from contamination by truncated species. We have developed a method to invert DNA molecules in situ after completed synthesis. Reactive functions at the 5'-ends of the oligonucleotides are permitted to react with functions on the support before the 3'-ends are releas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.24.4710
更新日期:1999-12-15 00:00:00
abstract::Single-nucleotide polymorphisms (SNPs) are often linked to critical phenotypes such as diseases or responses to vaccines, medications and environmental factors. However, the specific molecular mechanisms by which a causal SNP acts is usually not obvious. Changes in RNA secondary structure emerge as a possible explanat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1009
更新日期:2013-01-07 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 HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problema...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa980
更新日期:2021-01-08 00:00:00
abstract::The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1009
更新日期:2010-01-01 00:00:00
abstract::Galahad (https://galahad.esat.kuleuven.be) is a web-based application for analysis of drug effects. It provides an intuitive interface to be used by anybody interested in leveraging microarray data to gain insights into the pharmacological effects of a drug, mainly identification of candidate targets, elucidation of m...
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abstract::A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emissi...
journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::The mouse c-Ki-ras protooncogene promoter contains an unusual DNA element consisting of a 27 bp-long homopurine-homopyrimidine mirror repeat (H-motif) adjacent to a d(C-G)5 repeat. We have previously shown that in vitro these repeats may adopt H and Z conformations, respectively, causing nuclease and chemical hypersen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.16.3271
更新日期:1994-08-25 00:00:00
abstract::The self-assembly of bis-biotinylated double-stranded DNA and the tetravalent biotin-binding protein streptavidin (STV) have been studied by non-denaturing gel electrophoresis and atomic force microscopy (AFM). The rapid self-assembly reproducibly generated populations of individual oligomeric complexes. Most striking...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.23.4553
更新日期:1999-12-01 00:00:00
abstract::The RES complex was previously identified in yeast as a splicing factor affecting nuclear pre-mRNA retention. This complex was shown to contain three subunits, namely Snu17, Bud13 and Pml1, but its mode of action remains ill-defined. To obtain insights into its function, we have performed a structural investigation of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn894
更新日期:2009-01-01 00:00:00
abstract::Many, if not all, mRNAs in T.brucei start with the same sequence of 35 nucleotides, separately encoded in clustered so-called mini-exon repeats. From these mini-exon repeats a 141-nt precursor RNA with the 35-nt sequence at its 5' end is transcribed. Indirect evidence suggests that this RNA is linked in a second step ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.24.9457
更新日期:1984-12-21 00:00:00
abstract::Sequences from -3500 to +1365 of the chicken histone H5 gene have been analyzed for the presence of cis-acting elements in H5 expressing (transformed CFU-E) and non-expressing cells (fibroblasts). The region from -3500 to -115 had little effect on transcription. Proximal upstream sequences contain a negative element (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.18.7495
更新日期:1989-09-25 00:00:00
abstract::DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku613
更新日期:2014-01-01 00:00:00
abstract::The rat alpha- and bovine alpha s1-casein genes have been isolated and their 5' sequences determined. The rat alpha-, beta-, gamma- and bovine alpha s1-casein genes contain similar 5' exon arrangements in which the 5' noncoding, signal peptide and casein kinase phosphorylation sequences are each encoded by separate ex...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.4.1883
更新日期:1986-02-25 00:00:00
abstract::Fundamental aspects of the biochemistry of Type III restriction endonucleases remain unresolved despite being characterized by numerous research groups in the past decades. One such feature is the subunit stoichiometry of these hetero-oligomeric enzyme complexes, which has important implications for the reaction mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku122
更新日期:2014-04-01 00:00:00
abstract::The carbon catabolite repressor protein 4 (Ccr4)-Negative on TATA (Not) complex controls gene expression at two levels. In the nucleus, it regulates the basal transcription machinery, nuclear receptor-mediated transcription and histone modifications. In the cytoplasm, the complex is required for messenger RNA (mRNA) t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr011
更新日期:2011-05-01 00:00:00