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 similarity, pharmacophores, fragment propensities and machine-learning models for the prediction of various toxicity endpoints; such as acute toxicity, hepatotoxicity, cytotoxicity, carcinogenicity, mutagenicity, immunotoxicity, adverse outcomes pathways (Tox21) and toxicity targets. The predictive models are built on data from both in vitro assays (e.g. Tox21 assays, Ames bacterial mutation assays, hepG2 cytotoxicity assays, Immunotoxicity assays) and in vivo cases (e.g. carcinogenicity, hepatotoxicity). The models have been validated on independent external sets and have shown strong performance. ProTox-II provides a freely available webserver for in silico toxicity prediction for toxicologists, regulatory agencies, computational and medicinal chemists, and all users without login at http://tox.charite.de/protox_II. The webserver takes a two-dimensional chemical structure as an input and reports the possible toxicity profile of the chemical for 33 models with confidence scores, and an overall toxicity radar chart along with three most similar compounds with known acute toxicity.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Banerjee P,Eckert AO,Schrey AK,Preissner Rdoi
10.1093/nar/gky318subject
Has Abstractpub_date
2018-07-02 00:00:00pages
W257-W263issue
W1eissn
0305-1048issn
1362-4962pii
4990033journal_volume
46pub_type
杂志文章abstract::In the process of establishing more and more complete annotations of eukaryotic genomes, a constantly growing number of alternative splicing (AS) events has been reported over the last decade. Consequently, the increasing transcript coverage also revealed the real complexity of some variations in the exon-intron struc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm311
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abstract::Stacking self-association equilibria in aqueous solutions of m3uridine, m34,2',3',5'uridine, 2'-deoxyuridine, m13,4,4cytosine, m14,4,4,5cytosine, s2cytidine and s4thymidine were studied at various temperatures by vapour-pressure osmometry. Equilibrium constants Kst's were computed on the assumption of the isodesmic mo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.5.1295
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abstract::Mitochondrial-DNA diseases have no effective treatments. Allotopic expression-synthesis of a wild-type version of the mutated protein in the nuclear-cytosolic compartment and its importation into mitochondria-has been proposed as a gene-therapy approach. Allotopic expression has been successfully demonstrated in yeast...
journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records incl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt911
更新日期:2014-01-01 00:00:00
abstract::Scalable and cost-effective production of error-free DNA is critical to meet the increased demand for such DNA in the field of biological science. Methods based on 'Dial-out PCR' have enabled the high-throughput error-free DNA synthesis from a microarray-synthesized DNA pool by labeling with retrieval PCR tags, and re...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2018-04-20 00:00:00
abstract::Originally identified as an RNA polymerase II interactor, Che-1/AATF (Che-1) has now been recognized as a multifunctional protein involved in cell-cycle regulation and cancer progression, as well as apoptosis inhibition and response to stress. This protein displays a peculiar nucleolar localization and it has recently...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa344
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journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.8.1851
更新日期:2002-04-15 00:00:00
abstract::We had shown previously (3) that the E. coli argE gene could be turned-on by an IS3 element inserted in orientation II near the 5' end of the gene. Here we show that this effect is due to the presence of an outward promoter located on IS3. The exact site of insertion of IS3 was determined by DNA sequencing. Using the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.19.5935
更新日期:1982-10-11 00:00:00
abstract::A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Base...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.suppl.r403
更新日期:1988-01-01 00:00:00
abstract::The chloroplast ribosomal protein CS1 is an essential component of the plastids translational machinery involved in translation initiation. Southern analysis suggests that the corresponding nuclear gene is present in one copy in the spinach genome. We have isolated and sequenced the gene (rps1) to study its expression...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.16.4153
更新日期:1992-08-25 00:00:00
abstract::We have examined the interactions of UvrABC endonuclease with DNA containing the monoadducts of 8-methoxypsoralen (8-MOP) and 4,5',8-trimethylpsoralen (TMP). The UvrA and UvrB proteins were found to form a stable complex on DNA that contains the psoralen monoadducts. Subsequent binding of UvrC protein to this complex ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.12.4957
更新日期:1987-06-25 00:00:00
abstract::Cloned ribosomal DNA (rDNA) of Locusta migratoria was analyzed by restriction site mapping and SI nuclease experiments. The repeat unit is 18 kb long. The nontranscribed spacer region (NTS) is very large (11 kb) and homogeneous in length, but many of the restriction sites are heterogeneous among the repeat units. Two ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.4.1251
更新日期:1985-02-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.22.4542
更新日期:1995-11-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr795
更新日期:2012-02-01 00:00:00
abstract::Triethylammonium uridine-3',5'-cyclic phosphorothioate crystallizes in space group P2(1)2(1)2(1), a = 7.177(1), b = 13.155(6), c = 21.114(7) A, C15H26N3O7PS, MW 423.4, Z = 4, dx = 1.41g/cm3. The crystal structure was solved by direct methods on the basis of 1493 counter X-ray diffraction data (CuK alpha) and refined t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.12.4945
更新日期:1987-06-25 00:00:00
abstract::Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests putative homing endonuclease (HEase) genes. Here, we report the identification and characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeKI [corrected], encoded by the ApeK1.S908 intron within the 16S rDNA of Aeropyrum...
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更新日期:2005-07-26 00:00:00
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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更新日期:1997-10-01 00:00:00
abstract::The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and func...
journal_title:Nucleic acids research
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abstract::Negative superhelical strain induces the poly(dG)-poly(dC) sequence to adopt two totally different types of triple-helices, either a dG.dG.dC triplex in the presence of Mg(+)+ at both neutral and acidic pHs or a protonated dC+.dG.dC triplex in the absence of Mg(+)+ ions at acidic pH (1). To examine whether there are s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.15.4267
更新日期:1991-08-11 00:00:00
abstract::Topoisomerase II, purified from chicken erythrocytes, was reacted with a large number of different DNA fragments and cleavages were catalogued in the presence and absence of drugs that stabilize the cleavage intermediate. Cleavages were sequenced to derive a consensus for topoisomerase II that predicts catalytic sites...
journal_title:Nucleic acids research
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abstract::A class II site-specific endodeoxyribonuclease (SalPI) was identified in cell-free extracts of Streptomyces albus CMI 52766 after high speed centrifugation and fractionation through Bio Gel AO.5M. SalPI cleaves lambda DNA into at least 18 fragments. Five cleavage sites were located in the linear lambda map by the use ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.6.1989
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abstract::The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. RdRPs are essential in virus life cycle due to their central role in viral genome replication/transcription processes. However, their contribution in host adaption has not been well documented. By sol...
journal_title:Nucleic acids research
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abstract::The role of thymine dimerization for previously reported U.V. induced conformational changes has been proved using acetophenone as sensitizer for the specific thymine dimerization upon irradiation at 313 nm. CD results demonstrate that formation of pyrimidine dimers cause typical conformational changes of the DNA B he...
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更新日期:2006-01-13 00:00:00
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