Abstract:
:Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein-protein interactions (>30 000) and PTMs (>8000) for human proteins. We have also introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer (http://www.genprot.org), developed by us that allows integration of genomic and proteomic information. With the continued support and active participation by the biomedical community, we expect HPRD to become a unique source of curated information for the human proteome and spur biomedical discoveries based on integration of genomic, transcriptomic and proteomic data.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Mishra GR,Suresh M,Kumaran K,Kannabiran N,Suresh S,Bala P,Shivakumar K,Anuradha N,Reddy R,Raghavan TM,Menon S,Hanumanthu G,Gupta M,Upendran S,Gupta S,Mahesh M,Jacob B,Mathew P,Chatterjee P,Arun KS,Sharma S,Chanddoi
10.1093/nar/gkj141keywords:
subject
Has Abstractpub_date
2006-01-01 00:00:00pages
D411-4issue
Database issueeissn
0305-1048issn
1362-4962pii
34/suppl_1/D411journal_volume
34pub_type
杂志文章abstract::Type IIS restriction endonuclease BtsCI (GGATG 2/0) is a neoschizomer of FokI (GGATG 9/13) and cleaves closer to the recognition sequence. Although M.BtsCI shows 62% amino acid sequence identity to M.FokI, BtsCI and FokI restriction endonucleases do not share significant amino acid sequence similarity. BtsCI belongs t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1092
更新日期:2010-03-01 00:00:00
abstract::Two models have been proposed for triggering release of the lagging strand polymerase at the replication fork, enabling cycling to the primer for the next Okazaki fragment--either collision with the 5'-end of the preceding fragment (collision model) or synthesis of a new primer by primase (signaling model). Specific p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1098
更新日期:2014-02-01 00:00:00
abstract::A method for constructing yeast artificial chromosome (YAC) libraries with large insert sizes is reported. High molecular weight human DNA was partially digested with EcoRI and cloned in the vector pYAC4. When unfractionated DNA was used, the mean YAC size was 120kb. Fractionation by pulsed-field gel electrophoresis u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.9.3425
更新日期:1989-05-11 00:00:00
abstract::Nucleotide sequences of three cloned restriction fragments of Tetrahymena mtDNA which showed hybridization with mitochondrial tRNA have been determined. EcoRI fragment 5 (4.1 kbp) contains the tRNAphe gene sequence with anticodon GAA; Hind III fragment 6 (2.0 kbp) the tRNAhis with anticodon GTG; and EcoRI fragment 7 (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.9.3273
更新日期:1985-05-10 00:00:00
abstract::Eucaryotic transcription initiation by RNA polymerase II involves protein:DNA interactions during the formation of a transcription complex. In addition to RNA polymerase II there are at least five other general transcription factors necessary for initiation with the adenovirus major late promoter. One of these, TFIIA,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.12.3611
更新日期:1990-06-25 00:00:00
abstract::Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1296
更新日期:2013-02-01 00:00:00
abstract::We recently reported that the antitumor triazoloacridone, compound C-1305, is a topoisomerase II poison with unusual properties. In this study we characterize the DNA interactions of C-1305 in vitro, in comparison with other topoisomerase II inhibitors. Our results show that C-1305 binds to DNA by intercalation and po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki904
更新日期:2005-10-27 00:00:00
abstract::The DNA photosensitisers m-iodo Hoechst and m-iodo, p-methoxy Hoechst have been co-crystallised with the oligonucleotide d(CGCGAATTCGCG)(2)and their crystal structures determined. The crystals were then subjected to slow dehydration, which reduced their solvent contents from 40 (normal) to 30 (partially dehydrated) an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.5.1252
更新日期:2000-03-01 00:00:00
abstract::The transcription regulator, tvMyb1, is the first Myb family protein identified in Trichomonas vaginalis. Using an electrophoretic mobility shift assay, we defined the amino-acid sequence from Lys(35) to Ser(141) (tvMyb1(35-141)) as the minimal DNA-binding domain, encompassing two Myb-like DNA-binding motifs (designat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp097
更新日期:2009-04-01 00:00:00
abstract::Cells respond to DNA damage by activating both cellular growth arrest and DNA repair processes. In Saccharomyces cerevesiae the RAD9 gene controls DNA damage-mediated cell cycle arrest that is known to allow efficient repair. To ascertain whether RAD9 plays a role in DNA repair per se, the removal of UV-induced photol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.10.2020
更新日期:2001-05-15 00:00:00
abstract::Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt177
更新日期:2013-05-01 00:00:00
abstract::Giant viruses have extraordinarily large dsDNA genomes, and exceptionally, they encode various components of the translation apparatus, including tRNAs, aminoacyl-tRNA synthetases and translation factors. Here, we focused on the elongation factor 1 (EF1) family of viral translational GTPases (trGTPases), using computa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz296
更新日期:2019-06-20 00:00:00
abstract::The active and inactive state of transcription factors in growing cells is usually directed by allosteric physicochemical signals or metabolites, which are in turn either produced in the cell or obtained from the environment by the activity of the products of effector genes. To understand the regulatory dynamics and t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm743
更新日期:2007-01-01 00:00:00
abstract::In the present study, the relationship between short interfering RNA (siRNA) sequence and RNA interference (RNAi) effect was extensively analyzed using 62 targets of four exogenous and two endogenous genes and three mammalian and Drosophila cells. We present the rules that may govern siRNA sequence preference and in a...
journal_title:Nucleic acids research
pub_type: 指南,杂志文章
doi:10.1093/nar/gkh247
更新日期:2004-02-09 00:00:00
abstract::An adequate supply of nucleotides is essential for DNA replication and DNA repair. Moreover, inhibition of TTP synthesis can cause cell death by a poorly characterized mechanism called thymine-less death. In the yeast Saccharomyces cerevisiae, the genes encoding thymidylate synthetase (CDC21) and thymidylate kinase (C...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki219
更新日期:2005-01-28 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
pub_type: 杂志文章
doi:10.1093/nar/gkz936
更新日期:2019-12-02 00:00:00
abstract::The TGGCA protein, the chicken homologue of HeLa cell NF-I, was purified to homogeneity from liver tissue by a procedure which includes preparative mobility shift electrophoresis (PMSE) as the final step. PMSE was here adjusted for the isolation of the TGGCA protein, but can be used as a general method to characterize...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.23.9707
更新日期:1987-12-10 00:00:00
abstract::The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt977
更新日期:2014-01-01 00:00:00
abstract::MODPROPEP is a web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases. The available crystal structures of protein-peptide complexes in PDB are used as templates for modeling peptides of desired sequence in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm266
更新日期:2007-07-01 00:00:00
abstract::The Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp936
更新日期:2010-01-01 00:00:00
abstract::A short histone-like fusion RNA, generated when the RNA 3' processing signal from a mouse histone H4 gene is inserted into a heterologous transcription unit, becomes correctly down-regulated in G1-arrested cells of a temperature-sensitive mouse mastocytoma cell cycle mutant (21-Tb; Stauber et al., EMBO J. 5, 3297-3303...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9399
更新日期:1988-10-25 00:00:00
abstract::Bacterial RNase III plays important roles in the processing and degradation of RNA transcripts. A major goal is to identify the cleavage targets of this endoribonuclease at a transcriptome-wide scale and delineate its in vivo cleavage rules. Here we applied to Escherichia coli grown to either exponential or stationary...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky684
更新日期:2018-11-02 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
pub_type: 杂志文章
doi:10.1093/nar/gki487
更新日期:2005-07-01 00:00:00
abstract::A fraction of the ribosomal 28S genes in some insects are interrupted at specific sites by insertion elements R1 and R2 (also called Type I and II). These elements contain long open-reading frames with homology to reverse transcriptase. We have identified in the silkmoth, Bombyx mori, copies of these elements which ha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.22.10561
更新日期:1988-11-25 00:00:00
abstract::In eukaryotic cells, the shortening and removal of the poly(A) tail of cytoplasmic mRNA by deadenylase enzymes is a critical step in post-transcriptional gene regulation. The ribonuclease activity of deadenylase enzymes is attributed to either a DEDD (Asp-Glu-Asp-Asp) or an endonuclease-exonuclease-phosphatase domain....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt972
更新日期:2014-03-01 00:00:00
abstract::We present evidence that the splice sites in mammalian pre-mRNAs are brought together via a three dimensional diffusion mechanism. We tested two mechanisms for splice site pairing: a lateral diffusion ('scanning') model and the currently favored three dimensional diffusion ('jumping') model. Two lines of evidence that...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.9.1638
更新日期:1996-05-01 00:00:00
abstract::Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein-protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq481
更新日期:2010-07-01 00:00:00
abstract::Abasic substitutions in the non-template strand and promoter sequence changes were made to assess the roles of various promoter features in sigma70 holoenzyme interactions with fork junction probes. Removal of -10 element non-template single strand bases, leaving the phosphodiester backbone intact, did not interfere w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg400
更新日期:2003-06-01 00:00:00
abstract::Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itse...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1167
更新日期:2019-02-20 00:00:00
abstract::This work presents a neutral filter elution method for detecting DNA double strand breaks in mouse L1210 cells after X-ray. The assay will detect the number of double strand breaks induced by as little as 1000 rad of X-ray. The rate of DNA elution through the filters under neutral conditions increases with X-ray dose....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.3.793
更新日期:1979-10-10 00:00:00