Abstract:
:Small disulfide-bonded proteins (SDPs) are rich sources for therapeutic drugs. Designing drugs from these proteins requires three-dimensional structural information, which is only available for a subset of these proteins. SDPMOD addresses this deficit in structural information by providing a freely available automated comparative modeling service to the research community. For expert users, SDPMOD offers a manual mode that permits the selection of a desired template as well as a semi-automated mode that allows users to select the template from a suggested list. Besides the selection of templates, expert users can edit the target-template alignment, thus allowing further customization of the modeling process. Furthermore, the web service provides model stereochemical quality evaluation using PROCHECK. SDPMOD is freely accessible to academic users via the web interface at http://proline.bic.nus.edu.sg/sdpmod.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kong L,Lee BT,Tong JC,Tan TW,Ranganathan Sdoi
10.1093/nar/gkh394keywords:
subject
Has Abstractpub_date
2004-07-01 00:00:00pages
W356-9issue
Web Server issueeissn
0305-1048issn
1362-4962pii
32/suppl_2/W356journal_volume
32pub_type
杂志文章abstract::Mitochondrial DNA is a sensitive target of chemical carcinogens (Backer and Weinstein (1980) Science 209, 297-299), suggesting that mutations of the mitochondrial genome occur in tumor cells. We examined this point by comparing mitochondrial DNA sequences in four rat tumors with those of normal rat liver. Some novel m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.6.1635
更新日期:1983-03-25 00:00:00
abstract::Clustered damages are formed in DNA by ionising radiation and radiomimetic anticancer agents and are thought to be biologically severe. 7,8-dihydro-8-oxoguanine (8-oxoG), a major DNA damage resulting from oxidative attack, is highly mutagenic leading to a high level of G.C-->T.A transversions if not previously excised...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.5.1107
更新日期:2001-03-01 00:00:00
abstract::The binding of transposase (Tnp) to the specific Tn5 end sequences is the first dedicated reaction during transposition. In this study, comparative DNA-binding analyses were performed using purified full-length Tnp and a C-terminal deletion variant (delta369) that lacks the putative dimerization domain. The shape of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.19.3790
更新日期:1996-10-01 00:00:00
abstract::Saccharomyces cerevisiae Pif1 (ScPif1) is known as an ATP-dependent DNA helicase that plays critical roles in a number of important biological processes such as DNA replication, telomere maintenance and genome stability maintenance. Besides its DNA helicase activity, ScPif1 is also known as a single-stranded DNA (ssDN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz541
更新日期:2019-08-22 00:00:00
abstract::The repetitive zinc finger domain of transcription factor IIIA binds 5S DNA and 5S RNA with similar affinity. Site directed mutagenesis of the Xenopus borealis somatic 5S RNA gene has been used to produce a series of derivatives of 5S RNA containing local sequence substitutions or sequence deletions. Gel mobility shif...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.11.2639
更新日期:1992-06-11 00:00:00
abstract::The cDNA encoding the human RNA lariat debranching enzyme (hDBR1) was identified and cloned by searching the Expressed Sequence Tag (EST) database and screening a HeLa cDNA library, based on predicted amino acid sequence homologies with the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Caenorhabditis elegans...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.18.3666
更新日期:2000-09-15 00:00:00
abstract::Rad18 is a ubiquitin E3 ligase that monoubiquitinates PCNA on stalled replications forks. This allows recruitment of damage-tolerant polymerases for damage bypass and DNA repair. In this activity, the Rad18 protein has to interact with Rad6, the E2 ubiquitin-conjugating enzyme, ubiquitin, PCNA and DNA. Here we analyze...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm615
更新日期:2007-01-01 00:00:00
abstract::MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target inte...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1258
更新日期:2016-01-04 00:00:00
abstract::Mutant AraC proteins were selected for their ability to induce but not to repress, or their ability to repress but not to induce the araBAD operon. One such unusual mutant is able to bind to the araI site with an affinity only two to three-fold weaker than the wild type AraC protein, but the mutant protein was shown, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.14.5019
更新日期:1985-07-25 00:00:00
abstract::Signal transducer and activator of transcription 6 (STAT6) is a regulator of transcription for interleukin-4 (IL-4)-induced genes. The ability of STAT6 to activate transcription depends on functional interaction with other transcription factors and coactivators. We have characterized the mechanism of STAT6-mediated tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl539
更新日期:2006-01-01 00:00:00
abstract::The synthesis of ribosomal precursor RNA in Novikoff hepatoma (N1S1) cells is very sensitive to cordycepin (3'-dA). The synthesis of hnRNA, however, is resistant to inhibition concentrations of 3'-dA that completely block the synthesis of 45S ribosomal RNA precursor. We have examined the RNA polymerases present in the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.2.325
更新日期:1976-02-01 00:00:00
abstract::Human immunodeficiency virus-1 (HIV-1) leader RNA, which contains double-stranded regions due to inverted repeats, was shown to activate the dsRNA-dependent enzymes associated with the interferon system. HIV-1 leader RNA produced in vitro using SP6 RNA polymerase was characterized using probes for antisense and sense-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.3.969
更新日期:1989-02-11 00:00:00
abstract::Previous work has demonstrated that the yeast SPT3 gene is required for transcription from delta sequences, the long terminal repeats that flank yeast Ty elements. In spt3 null mutants, transcription fails to initiate in delta sequences and instead initiates farther downstream. Null mutations in SPT3 cause other mutan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.17.6885
更新日期:1986-09-11 00:00:00
abstract::A protein-DNA complex has less gel electrophoretic mobility than the free DNA fragment. One parameter for the degree of retardation of a linear DNA fragment in a protein-DNA complex is the molecular weight of the bound protein(s). The quotient of the migration distances of free DNA (m) and protein-DNA complex (m') is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.12.5241
更新日期:1988-06-24 00:00:00
abstract::Activating sequence factor 1 (ASF-1) is a nuclear DNA-binding activity that is found in monocots and dicots. It interacts with several TGACG-containing elements that have been characterized from viral and T-DNA genes, the prototypes of which are the as-1 element of the CaMV 35S promoter and the ocs element from the oc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.18.3778
更新日期:1995-09-25 00:00:00
abstract::Complex carbohydrates are known as mediators of complex cellular events. Concerning their structural diversity, their potential of information content is several orders of magnitude higher in a short sequence than any other biological macromolecule. SWEET-DB (http://www.dkfz.de/spec2/sweetdb/) is an attempt to use mod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.405
更新日期:2002-01-01 00:00:00
abstract::Plant orthologs of the yeast sucrose non-fermenting (Snf1) kinase and mammalian AMP-activated protein kinase (AMPK) represent an emerging class of important regulators of metabolic and stress signalling. The catalytic alpha-subunits of plant Snf1-related kinases (SnRKs) interact in the yeast two-hybrid system with dif...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.17.3685
更新日期:2001-09-01 00:00:00
abstract::Non-protein-coding RNAs (ncRNAs) fulfill a wide range of cellular functions from protein synthesis to regulation of gene expression. Identification of novel regulatory ncRNAs by experimental approaches commonly includes the generation of specialized cDNA libraries encoding small ncRNA species. However, such identifica...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm244
更新日期:2007-01-01 00:00:00
abstract::A C-->U mutation (rdn5) in the conserved sarcin/ricin domain of yeast 25S rRNA has been shown to cause translational suppression and paromomycin resistance. It also separates the killing from the misreading effect of this antibiotic. We confirm these findings and provide in vitro evidence that rdn5 causes a 3-fold inc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh860
更新日期:2004-10-11 00:00:00
abstract::Evidence will be presented to show that the allyl group is suitable for the protection of a 3'-terminal phosphodiester function. The latter will be demonstrated by the synthesis, via a phosphotriester approach, of two cyclic tetraribonucleotides [r(AAAA) and r(UAMe2UAMe2)], two cyclic hexadeoxyribonucleotides [d(CGCGC...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4607
更新日期:1988-05-25 00:00:00
abstract::DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, the experimental implementation of in silico circuit designs has been hindered by the problem of circuit leakage. Here, we systematically an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw447
更新日期:2016-08-19 00:00:00
abstract::Transcription factor IIIA (TFIIIA) is specifically required for transcription of 5S rRNA genes and is the archetypal C2H2 zinc finger protein. All known vertebrate TFIIIAs have a similar organization: nine zinc fingers, followed by a C-terminal domain of unknown structure. The zinc fingers of Saccharomyces cerevisiae ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf385
更新日期:2002-07-01 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::We have recently isolated a functional promoter encoding the human polypeptide-binding protein (BiP) gene from Burkitt's lymphoma cells by polymerase chain reaction (The EMBL Data Library accession number X59969, 1991). This promoter DNA segment (termed BiP670) was fused to the bacterial chloramphenicol acetyltransfer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.24.6481
更新日期:1992-12-25 00:00:00
abstract::The Bayesian regularization method for high-throughput differential analysis, described in Baldi and Long (A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001: 17: 509-519) and implemented in the Cyber-T web server, is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks420
更新日期:2012-07-01 00:00:00
abstract::We studied the interaction of ethidium bromide with rye and calf thymus chromatin. Both types of chromatin have the same dye accessibility, which is about 50% of that of DNA. From this result we conclude that the molecular structure of these two chromatins is similar. For rye, the extraction of H1 produces no change i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.9.2193
更新日期:1976-09-01 00:00:00
abstract::Prostatic steroid binding protein, whose expression is stimulated by androgens, consists of two subunits: one containing the polypeptides C1 and C3 and the other containing C2 and C3. We have characterised genomic clones containing the C1 and C2 genes by restriction enzyme analysis and DNA sequencing. Both genes are 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.17.5121
更新日期:1982-09-11 00:00:00
abstract::Four pseudorevertants of a -10 region lacP mutation were isolated. Three of these mutations were found to activate nascent promoters. These mutations were: a -2 G/C----A/T change (-2A) promoting transcription at position +11, a +1 A/T----T/A change (+1T) promoting transcription initiation at position +13, and a +10 C/...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.10.3927
更新日期:1989-05-25 00:00:00
abstract::The positive role of PARP1 in regulation of various nuclear DNA transactions is well established. Although a mitochondrial localization of PARP1 has been suggested, its role in the maintenance of the mitochondrial DNA is currently unknown. Here we investigated the role of PARP1 in the repair of the mitochondrial DNA i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1089
更新日期:2014-12-01 00:00:00
abstract::Replacement of alpha-, beta- and gamma-phosphate groups in 2'-deoxynucleoside 5'-triphosphates (dNTP) with phosphonate groups yields a new set of dNTP mimics with potential biological and therapeutic applications. Here, we describe the synthesis of 15 new dNTPs modified at alpha-, beta- and gamma-phosphates containing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.3.778
更新日期:1998-02-01 00:00:00