PI2PE: protein interface/interior prediction engine.

abstract：:The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes,...

journal_title：Nucleic acids research

authors： Howe DG,Ramachandran S,Bradford YM,Fashena D,Toro S,Eagle A,Frazer K,Kalita P,Mani P,Martin R,Moxon ST,Paddock H,Pich C,Ruzicka L,Schaper K,Shao X,Singer A,Van Slyke CE,Westerfield M

更新日期：2021-01-08 00:00:00

abstract：:The task of gene identification frequently confronting researchers working with both novel and well studied genomes can be conveniently and reliably solved with the help of the GeneMark web software (http://opal.biology.gatech.edu/GeneMark/). The website provides interfaces to the GeneMark family of programs designed ...

journal_title：Nucleic acids research

authors： Besemer J,Borodovsky M

更新日期：2005-07-01 00:00:00

abstract：:Serine integrases are emerging as core tools in synthetic biology and have applications in biotechnology and genome engineering. We have designed a split-intein serine integrase-based system with potential for regulation of site-specific recombination events at the protein level in vivo. The ϕC31 integrase was split i...

journal_title：Nucleic acids research

authors： Olorunniji FJ,Lawson-Williams M,McPherson AL,Paget JE,Stark WM,Rosser SJ

更新日期：2019-12-02 00:00:00

abstract：:We have previously mapped a repression domain from the active transcriptional repressor E4BP4 to a 65 amino acid segment near the C-terminus of the polypeptide. Here we show that the E4BP4 repression domain interacts specifically with the TBP binding repressor protein Dr1. Mutants that affect the ability of E4BP4 to b...

journal_title：Nucleic acids research

authors： Cowell IG,Hurst HC

更新日期：1996-09-15 00:00:00

abstract：:A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoa...

journal_title：Nucleic acids research

authors： Lahoud G,Timoshchuk V,Lebedev A,Arar K,Hou YM,Gamper H

更新日期：2008-12-01 00:00:00

abstract：:Rad2/XPG belongs to the flap nuclease family and is responsible for a key step of the eukaryotic nucleotide excision DNA repair (NER) pathway. To elucidate the mechanism of DNA binding by Rad2/XPG, we solved crystal structures of the catalytic core of Rad2 in complex with a substrate. Rad2 utilizes three structural mo...

journal_title：Nucleic acids research

authors： Miętus M,Nowak E,Jaciuk M,Kustosz P,Studnicka J,Nowotny M

更新日期：2014-01-01 00:00:00

abstract：:A peculiar phenomenon is observed in several adenovirus type 2 or 5 (Ad2 or Ad5) transformed cell lines: the right hand and left hand terminal regions of the viral genome present in the viral DNA insertions of these cell lines are found to be linked together. A large part of the viral DNA insertion present in the Ad5 ...

journal_title：Nucleic acids research

authors： Visser L,Reemst AC,van Mansfeld AD,Rozijn TH

更新日期：1982-04-10 00:00:00

abstract：:Fully modified 4'-thioDNA, an oligonucleotide only comprising 2'-deoxy-4'-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4'-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4'-thioDNA was found to behave like an...

journal_title：Nucleic acids research

authors： Matsugami A,Ohyama T,Inada M,Inoue N,Minakawa N,Matsuda A,Katahira M

更新日期：2008-04-01 00:00:00

abstract：:Initiation of reverse transcription is a complex and regulated process in all retroviruses. Several base pairing interactions have been proposed to occur between the HIV-1 RNA genome and the specific tRNA(lys3) primer. The tRNA primer can form up to 21 bp with the primer binding site (PBS), and an additional 8 bp inte...

journal_title：Nucleic acids research

authors： Huthoff H,Bugala K,Barciszewski J,Berkhout B

更新日期：2003-09-01 00:00:00

abstract：:2'-O-(2-methoxyethyl) (2'-MOE) RNA possesses favorable pharmocokinetic properties that make it a promising option for the design of oligonucleotide drugs. Telomerase is a ribonucleoprotein that is up-regulated in many types of cancer, but its potential as a target for chemotherapy awaits the development of potent and ...

journal_title：Nucleic acids research

authors： Elayadi AN,Demieville A,Wancewicz EV,Monia BP,Corey DR

更新日期：2001-04-15 00:00:00

abstract：:P53-binding protein 1 (53BP1) mediates DNA repair pathway choice and promotes checkpoint activation. Chromatin marks induced by DNA double-strand breaks and recognized by 53BP1 enable focal accumulation of this multifunctional repair factor at damaged chromatin. Here, we unveil an additional level of regulation of 53B...

journal_title：Nucleic acids research

authors： Salvador Moreno N,Liu J,Haas KM,Parker LL,Chakraborty C,Kron SJ,Hodges K,Miller LD,Langefeld C,Robinson PJ,Lelièvre SA,Vidi PA

更新日期：2019-04-08 00:00:00

abstract：:RNA editing in protozoan parasites is a mitochondrial RNA processing reaction in which exclusively uridylate residues are inserted into, and less frequently deleted from, pre-mRNAs. Molecules central to the process are so-called guide RNAs (gRNAs) which function as templates in the reaction. For a detailed molecular u...

journal_title：Nucleic acids research

authors： Hermann T,Schmid B,Heumann H,Göringer HU

更新日期：1997-06-15 00:00:00

abstract：:Two analog uridine triphosphates tethering additional functionality, one a primary amino group and the second a mercapto group, were prepared and tested for their compatibility with in vitro RNA selection procedures. 5-(3-Aminopropyl)uridine triphosphate (UNH(2)) as a uridine substitute was a more effective substrate ...

journal_title：Nucleic acids research

authors： Vaish NK,Fraley AW,Szostak JW,McLaughlin LW

更新日期：2000-09-01 00:00:00

abstract：:We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify th...

journal_title：Nucleic acids research

authors： Moretti S,Reinier F,Poirot O,Armougom F,Audic S,Keduas V,Notredame C

更新日期：2006-07-01 00:00:00

abstract：:The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls:...

journal_title：Nucleic acids research

authors： Jónsson SR,Haché G,Stenglein MD,Fahrenkrug SC,Andrésdóttir V,Harris RS

更新日期：2006-01-01 00:00:00

abstract：:A multipurpose plasmid, pUR 250, has been constructed. It contains seven unique cloning sites (Hind III, Xba I, Sal I, Acc I, Hinc II, BamH I and EcoR I) in a small region of its lac Z gene part. Insertion of foreign DNA into the plasmid can be easily detected. Plasmid DNA isolated from a clone by a rapid method can b...

journal_title：Nucleic acids research

authors： Rüther U

更新日期：1982-10-11 00:00:00

abstract：:We have previously shown that Y box-binding protein-1 (YB-1) binds preferentially to cisplatin-modified Y box sequences. Based on structural and biochemical data, we predicted that this protein binds single-stranded nucleic acids. In the present study we confirmed the prediction and also discovered some unexpected fun...

journal_title：Nucleic acids research

authors： Izumi H,Imamura T,Nagatani G,Ise T,Murakami T,Uramoto H,Torigoe T,Ishiguchi H,Yoshida Y,Nomoto M,Okamoto T,Uchiumi T,Kuwano M,Funa K,Kohno K

更新日期：2001-03-01 00:00:00

abstract：:The human Microprocessor complex cleaves primary microRNA (miRNA) transcripts (pri-miRNAs) to initiate miRNA synthesis. Microprocessor consists of DROSHA (an RNase III enzyme), and DGCR8. DROSHA contains two RNase III domains, RIIIDa and RIIIDb, which simultaneously cleave the 3p- and 5p-strands of pri-miRNAs, respect...

journal_title：Nucleic acids research

authors： Nguyen TL,Nguyen TD,Bao S,Li S,Nguyen TA

更新日期：2020-03-18 00:00:00

abstract：:An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA pr...

journal_title：Nucleic acids research

authors： Pokhrel N,Origanti S,Davenport EP,Gandhi D,Kaniecki K,Mehl RA,Greene EC,Dockendorff C,Antony E

更新日期：2017-09-19 00:00:00

abstract：:Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translato...

journal_title：Nucleic acids research

authors： Liu W,Xiang L,Zheng T,Jin J,Zhang G

更新日期：2018-01-04 00:00:00

abstract：:Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural product discovery by enabling the rapid investigation of secondary metabolic potential within microbial genome sequences. Grouping homologous BGCs into Gene Cluster Families (GCFs) facilitates mapping their architectural and taxonom...

journal_title：Nucleic acids research

authors： Kautsar SA,Blin K,Shaw S,Weber T,Medema MH

更新日期：2021-01-08 00:00:00

abstract：:A dnaB-like protein from P. aeruginosa was purified to near homogeneity using as an assay the immunoprecipitation by E. coli dnaB antiserum in a solid-phase. In the chromatographic characteristics including the affinity to immobilized ATP the dnaB-like protein of P. aeruginosa is similar to the dnaB protein of E. coli...

journal_title：Nucleic acids research

authors： Dreiseikelmann B,Riedel HD,Schuster H

更新日期：1987-01-26 00:00:00

abstract：:BsoFI , ItaI and Fsp4HI are isoshizomers of Fnu4HI (5'-GC NGC-3'). Both Fnu4HI and BsoFI have previously been shown to be inhibited by cytosine-specific methylation within the recognition sequence. Fnu4HI is inhibited if either the internal cytosine at position 2 or the external cytosine at position 5 of the restricti...

journal_title：Nucleic acids research

authors： Ramsahoye BH,Burnett AK,Taylor C

更新日期：1997-08-15 00:00:00

abstract：:Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, ...

journal_title：Nucleic acids research

authors： Spacková N,Sponer J

更新日期：2006-02-02 00:00:00

abstract：:TATA-binding protein (TBP) is central to the regulation of eukaryotic transcription initiation. Recruitment of TBP to target genes can be positively regulated by one of two basal transcription factor complexes: SAGA or TFIID. Negative regulation of TBP promoter association can be performed by Mot1p or the NC2 complex....

journal_title：Nucleic acids research

authors： Spedale G,Meddens CA,Koster MJ,Ko CW,van Hooff SR,Holstege FC,Timmers HT,Pijnappel WW

更新日期：2012-02-01 00:00:00

abstract：:The cancer drug daunomycin is an effective inhibitor of the B leads to Z transition in poly d(G-C) in 4 M NaCl. Both the rate and extent of the B leads to Z transition are decreased by the drug, as judged by equilibrium and kinetic studies. Daunomycin can, under some conditions, convert Z form DNA back to B form. Drug...

journal_title：Nucleic acids research

authors： Chaires JB

更新日期：1983-12-10 00:00:00

abstract：:The p-n-butylphenyl- and p-n-butylanilino- substituted analogs of dGTP and dATP, respectively, were tested as inhibitors of purified human placental DNA polymerases alpha and delta. It was observed that DNA polymerase alpha activity was potently inhibited by these analogs with I0.5 values as low as the nanomolar range...

journal_title：Nucleic acids research

authors： Lee MY,Toomey NL,Wright GE

更新日期：1985-12-09 00:00:00

abstract：:The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis gr...

journal_title：Nucleic acids research

authors： Rose S,Auxilien S,Havelund JF,Kirpekar F,Huber H,Grosjean H,Douthwaite S

更新日期：2020-07-09 00:00:00

abstract：:As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality fac...

journal_title：Nucleic acids research

authors： Schmalzing D,Belenky A,Novotny MA,Koutny L,Salas-Solano O,El-Difrawy S,Adourian A,Matsudaira P,Ehrlich D

更新日期：2000-05-01 00:00:00

abstract：:Simian virus 40 (SV40) nucleoprotein complexes were extracted from nuclei of infected monkey cells and fractionated on neutral sucrose density gradients. Complexes which contained replicating SV40 DNA (95S) separated well from those containing closed circular supercoiled viral DNA (75S). DNA polymerase activity was as...

journal_title：Nucleic acids research

authors： Otto B,Fanning E

更新日期：1978-05-01 00:00:00