Abstract:
:Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloSteric Database (ASD), the first online database that provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Currently, ASD contains 336 allosteric proteins from 101 species and 8095 modulators in three categories (activators, inhibitors and regulators). Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area. Integrating the information of allosteric proteins in ASD should allow for the identification of specific allosteric sites of a given subtype among proteins of the same family that can potentially serve as ideal targets for experimental validation. In addition, modulators curated in ASD can be used to investigate potent allosteric targets for the query compound, and also help chemists to implement structure modifications for novel allosteric drug design. Therefore, ASD could be a platform and a starting point for biologists and medicinal chemists for furthering allosteric research. ASD is freely available at http://mdl.shsmu.edu.cn/ASD/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Huang Z,Zhu L,Cao Y,Wu G,Liu X,Chen Y,Wang Q,Shi T,Zhao Y,Wang Y,Li W,Li Y,Chen H,Chen G,Zhang Jdoi
10.1093/nar/gkq1022subject
Has Abstractpub_date
2011-01-01 00:00:00pages
D663-9issue
Database issueeissn
0305-1048issn
1362-4962pii
gkq1022journal_volume
39pub_type
杂志文章abstract::Homologous recombination is essential for the preservation of genome stability, thereby preventing cancer. The recombination protein RAD51 drives DNA strand exchange, which requires the assembly, rearrangement and disassembly of a RAD51 filament on DNA, coupled to ATP binding and hydrolysis. This process is facilitate...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr295
更新日期:2011-08-01 00:00:00
abstract::A very mild and efficient procedure has been developed for the preparation of C-5 substituted deoxyuridines. The substituent carries a masked primary aliphatic amino group. These compounds are readily converted into their phosphoramidites and can be used to prepare oligonucleotides carrying one or more aliphatic amino...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.12.4857
更新日期:1987-06-25 00:00:00
abstract::RJ2.2.5, a mutant derived from the human B-lymphoma cell, Raji, is unable to express the MHC class II genes because of a recessive transcriptional defect attributed to the lack of an activator function. We report the isolation of a RJ2.2.5 revertant, namely AR, in which the expression of the mRNAs encoded by these gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.3.381
更新日期:1993-02-11 00:00:00
abstract::A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs are used for its analysis. The programs have been written for the Apple II microcomputer. A minimum investment is require...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.1.39
更新日期:1982-01-11 00:00:00
abstract::REV1 and DNA Polymerase ζ (REV3 and REV7) play important roles in translesion DNA synthesis (TLS) in which DNA replication bypasses blocking lesions. REV1 and Polζ have also been implicated in promoting repair of DNA double-stranded breaks (DSBs). However, the mechanism by which these two TLS polymerases increase tole...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr769
更新日期:2012-01-01 00:00:00
abstract::Loss-of-function in melanocortin 1 receptor (MC1R), a GS protein-coupled receptor that regulates signal transduction through cAMP and protein kinase A (PKA) in melanocytes, is a major inherited melanoma risk factor. Herein, we report a novel cAMP-mediated response for sensing and responding to UV-induced DNA damage re...
journal_title:Nucleic acids research
pub_type: 杂志文章,收录出版
doi:10.1093/nar/gkw871
更新日期:2016-12-15 00:00:00
abstract::The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silence...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr551
更新日期:2011-10-01 00:00:00
abstract::Deletion of Hop2 in mice eliminates homologous chromosome synapsis and disrupts double-strand break (DSB) repair through homologous recombination. HOP2 in vitro shows two distinctive activities: when it is incorporated into a HOP2-MND1 complex it stimulates DMC1 and RAD51 recombination activities and the purified HOP2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1234
更新日期:2014-02-01 00:00:00
abstract::X chromosome inactivation results in the cis-limited inactivation of most, but not all, genes on one of the two X chromosomes in mammalian females. The molecular basis for inactivation is unknown. In order to examine the transcriptional activity of human X-linked genes, a series of mouse-human somatic cell hybrids und...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.14.4191
更新日期:1990-07-25 00:00:00
abstract::DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx385
更新日期:2017-07-03 00:00:00
abstract::Extracellular and intracellular barriers typically prevent non-viral gene vectors from having an effective transfection efficiency. Formulation of a gene delivery vehicle that can overcome the barriers is a key step for successful tissue regeneration. We have developed a novel core-shelled DNA nanoparticle by invoking...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni171
更新日期:2005-11-03 00:00:00
abstract::The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodies...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz574
更新日期:2019-08-22 00:00:00
abstract::The detailed conformational features and dynamics of the naturally occurring deoxyribotrinucleoside diphosphates d-TpTpT and d-TpTpC have been investigated at 20 degrees C and 80 degrees C in aqueous solution by nuclear magnetic resonance spectroscopy. The observed NMR parameters indicate that the conformational prope...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.11.4399
更新日期:1978-11-01 00:00:00
abstract::The ability to integrate 'omics' (i.e. transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs) across different 'omics' data types or multi-dimensional data including time ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw157
更新日期:2016-06-02 00:00:00
abstract::The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.11.4481
更新日期:1987-06-11 00:00:00
abstract::Restriction-free cloning (RF-cloning) is a PCR-based technology that expands on the QuikChange™ mutagenesis process originally popularized by Stratagene in the mid-1990s, and allows the insertion of essentially any sequence into any plasmid at any location. While RF-cloning is a powerful tool for the design of custom ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks396
更新日期:2012-07-01 00:00:00
abstract::Native nucleotides show a hyperbolic concentration dependence of the pre-steady-state rate of incorporation while maintaining concentration-independent amplitude due to fast, largely irreversible pyrophosphate release. The kinetics of 3'-azido-2',3'-dideoxythymidine (AZT) incorporation exhibit an increase in amplitude...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm695
更新日期:2007-01-01 00:00:00
abstract::Fluorescence anisotropy and fluorescence correlation spectroscopy measurements of rhodamine-labeled DNA oligonucleotide duplexes have been used to determine equilibrium binding constants for DNA binding of the prokaryotic transcription activator protein NtrC. Measurements were made with wild-type NtrC from Escherichia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.6.1373
更新日期:1998-03-15 00:00:00
abstract::The discontinuous synthesis of the complementary strands of polyoma DNA in isolated nuclei has been studied by hybridization techniques. The relative amounts of the newly synthesized complementary strands were compared by separately annealing them to denatured HpaII restriction fragments. In every case an excess (1.4-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.5.1449
更新日期:1977-01-01 00:00:00
abstract::We characterized and purified a protein from rat liver which specifically binds to a DNA motif present in a liver-specific enhancer of the rat tyrosine aminotransferase (TAT) gene, when offered as single-stranded DNA. Binding is highly sequence-specific and coincides with a region known to be essential for function of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.6.1243
更新日期:1992-03-25 00:00:00
abstract::Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centre of the ribosome. Here, we present the 2.2 A crystal structure of tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn922
更新日期:2009-02-01 00:00:00
abstract::The NusA protein is a universally conserved bacterial transcription elongation factor that binds RNA polymerase (RNAP). When functioning independently, NusA enhances intrinsic termination. Paradoxically, NusA stimulates the function of the N and Q antiterminator proteins of bacteriophage λ. The mechanistic basis for N...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw198
更新日期:2016-06-20 00:00:00
abstract::Establishment and differentiation of mammary alveoli during pregnancy are controlled by prolactin through the transcription factors STAT5A and STAT5B (STAT5), which also regulate temporal activation of mammary signature genes. This study addressed the question whether the methyltransferase and transcriptional co-activ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv776
更新日期:2015-10-15 00:00:00
abstract::Glutaminyl-tRNA synthetase from Deinococcus radiodurans possesses a C-terminal extension of 215 residues appending the anticodon-binding domain. This domain constitutes a paralog of the Yqey protein present in various organisms and part of it is present in the C-terminal end of the GatB subunit of GatCAB, a partner of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1164
更新日期:2007-01-01 00:00:00
abstract::We report the first investigation of oligoribonucleotides containing a few 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine units (or 2'-hm-dT, abbreviated in this work as 'H'). Both the 2'-CH2O-phosphoramidite and 3'-O-phosphoramidite derivatives of H were synthesized and incorporated into both 2',5'-R...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki1003
更新日期:2005-12-23 00:00:00
abstract::A DNA copy of influenza A/NT/60/68 viral RNA segment 2, corresponding to protein P1, has been cloned in the E.coli plasmid pBr322. The clone is 2341 nucleotides long and represents a full-length copy of the viral RNA. In the viral complementary (plus sense) strand there is an open reading frame that is 2271 nucleotide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.4.1335
更新日期:1982-02-25 00:00:00
abstract::Accumulating evidence has demonstrated that transcriptional regulation is affected by DNA methylation. Understanding the perturbation of DNA methylation-mediated regulation between transcriptional factors (TFs) and targets is crucial for human diseases. However, the global landscape of DNA methylation-mediated transcr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa041
更新日期:2020-03-18 00:00:00
abstract::PRED(BALB/c) is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2(d) class I (H2-K(d), H2-L(d) and H2-D(d)) and class II (I-E(d) and I-A(d)) molecules. The p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki479
更新日期:2005-07-01 00:00:00
abstract::The National Center for Biotechnology Information (NCBI) Clone DB (http://www.ncbi.nlm.nih.gov/clone/) is an integrated resource providing information about and facilitating access to clones, which serve as valuable research reagents in many fields, including genome sequencing and variation analysis. Clone DB represen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1164
更新日期:2013-01-01 00:00:00
abstract::cDNA cloning is a central technology in molecular biology. cDNA sequences are used to determine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5'- and 3'-untranslated regions (UTRs). cDNA clones are valuable reagents for functional studies of genes and proteins. Expressed Sequen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni184
更新日期:2005-12-02 00:00:00