Abstract:
:For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein-ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23,269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Ahmed A,Smith RD,Clark JJ,Dunbar JB Jr,Carlson HAdoi
10.1093/nar/gku1088subject
Has Abstractpub_date
2015-01-01 00:00:00pages
D465-9issue
Database issueeissn
0305-1048issn
1362-4962pii
gku1088journal_volume
43pub_type
杂志文章abstract::The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1068
更新日期:2015-01-01 00:00:00
abstract::Proteomic and RNomic approaches have identified many components of different ribonucleoprotein particles (RNPs), yet still little is known about the organization and protein proximities within these heterogeneous and highly dynamic complexes. Here we describe a targeted cross-linking approach, which combines cross-lin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1366
更新日期:2016-02-18 00:00:00
abstract::Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv469
更新日期:2015-06-23 00:00:00
abstract::LNA oligonucleotides constitute a class of bicyclic RNA analogues having an exceptionally high affinity for their complementary DNA and RNA target molecules. We here report a novel method for highly efficient isolation of intact poly(A)+ RNA using an LNA-substituted oligo(dT) affinity ligand, based on the increased af...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh056
更新日期:2004-04-19 00:00:00
abstract::Replication Factor C (RF-C) of Saccharomyces cerevisiae is a complex that consists of several different polypeptides ranging from 120- to 37 kDa (Yoder and Burgers, 1991; Fien and Stillman, 1992), similar to human RF-C. We have isolated a gene, RFC2, that appears to be a component of the yeast RF-C. The RFC2 gene is l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.9.1527
更新日期:1994-05-11 00:00:00
abstract::We report thermodynamic values for binding of the guanosine nucleophile to the ribozyme derived from the Anabaena group I intron, and find that they are similar to those measured previously for the structurally distinct Tetrahymena ribozyme. The free energy of binding guanosine 5'-monophosphate (pG) at 30 degrees C is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.19.3722
更新日期:1996-10-01 00:00:00
abstract::The replication origin region of the Escherichia coli K-12 chromosome has been cloned, and a region of 245 base-pairs has been shown to contain all the information for autonomous replication (defined ori). In order to obtain further information on the sequence organization in the defined ori stretch, various types of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.12.3745
更新日期:1982-06-25 00:00:00
abstract::1,10-Phenanthroline-platinum(II)-ethylenediamine ( PEPt ) forms a crystalline complex with cytidine-3'-phosphate (3'-CMP) and its structure has been determined by X-ray crystallography. 3'-CMP molecules are hemiprotonated and form hydrogen-bonded pairs that stack above and below the phenanthroline-platinum(II) drug mo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.8.3649
更新日期:1984-04-25 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
pub_type: 杂志文章
doi:10.1093/nar/13.23.8623
更新日期:1985-12-09 00:00:00
abstract::The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw667
更新日期:2016-11-16 00:00:00
abstract::Single-molecule force spectroscopy provides insight into how proteins bind to and move along DNA. Such studies often embed a single-stranded (ss) DNA region within a longer double-stranded (ds) DNA molecule. Yet, producing these substrates remains laborious and inefficient, particularly when using the traditional thre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx761
更新日期:2017-10-13 00:00:00
abstract::DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 880 115 entries or 1 134 086 245 bases in the period from July 2006 to June 2007. The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others. Our computer system has been upgraded since March 2007. Anoth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm889
更新日期:2008-01-01 00:00:00
abstract::Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG(5)T, in ammonium acetate. The intermediates and products were separated according to their mass (number of strands and inner cations) and quantified. The study of the temporal ev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq208
更新日期:2010-08-01 00:00:00
abstract::The high mobility group protein (HMG)-box is a DNA-binding domain found in many proteins that bind preferentially to DNA of irregular structures in a sequence-independent manner and can bend the DNA. We show here that GST-fusion proteins of HMG domains from HMG1 and HMG2 promote a triple-stranded complex formation bet...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.23.4733
更新日期:1996-12-01 00:00:00
abstract::Interferons (IFNs) are a family of multifunctional proteins involved in immune activation, regulation of cell growth and antiviral response. They exert their functions by induction of several IFN-stimulated genes, including IFN regulatory factors (IRFs), a family of transcriptional regulators. One of these factors, IR...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.21.4219
更新日期:2000-11-01 00:00:00
abstract::We have developed a simple method to measure RNA synthesis in real time. In this technique, transcription reactions are performed in the presence of molecular beacons that possess a 2'-O-methylribonucleotide backbone. These probes become fluorescent as they hybridize to nascent RNA during the course of synthesis. We f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh068
更新日期:2004-05-20 00:00:00
abstract::To examine the influence of thyrotropin (TSH) on the thyroglobulin (Tgb) mRNA content, the latter was evaluated in the cytoplasm of hog thyroid cells cultured in the absence (control cells) or presence of TSH. The Tgb mRNA levels were determined by, (i) kinetics of hybridization to sheep Tgb cDNA, (ii) capacity of cod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.10.3353
更新日期:1979-07-25 00:00:00
abstract::DNA binding of heat shock factor 2 (HSF2) is induced during hemin-induced differentiation of human erythroleukemia cell line K562. To identify the transcriptional activation and the regulatory domains of HSF2, we constructed a series of deletion derivatives fused to the yeast GAL4 DNA binding domain and analyzed their...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2580
更新日期:1998-06-01 00:00:00
abstract::In fragile X syndrome, hypermethylation of the expanded CGG repeat and of the upstream promoter leads to transcriptional silencing of the FMR1 gene. Absence of the FMR1 protein results in mental retardation. We previously proved that treatment with 5-azadeoxycytidine (5-azadC) of fragile X cell lines results in reacti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf434
更新日期:2002-07-15 00:00:00
abstract::Denaturing gradient gel electrophoresis (DGGE) is based upon the different melting behaviors of DNA molecules in a chemical denaturant gradient according to their sequences. This technique has recently become a widespread tool to detect mutations. The introduction of a GC-clamp enables the detection of most single bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.12.3331
更新日期:1991-06-25 00:00:00
abstract::In this report we have analyzed the role of antisense transcription in the control of LEF1 transcription factor expression. A natural antisense transcript (NAT) is transcribed from a promoter present in the first intron of LEF1 gene and undergoes splicing in mesenchymal cells. Although this locus is silent in epitheli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv502
更新日期:2015-07-13 00:00:00
abstract::Nucleosomes released from oviduct nuclei during brief micrococcal nuclease digestions are enriched in transcribed sequences (bloom K.S. and Anderson, J.N. (1978) Cell, 15, 141-150). Such nucleosomes released into this 1Sf supernatant fraction are enriched in proteins HMG14, 17 and a third lower molecular weight protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.12.2761
更新日期:1981-06-25 00:00:00
abstract::The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq318
更新日期:2010-07-01 00:00:00
abstract::Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with DNA damage. Importantly...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkr697
更新日期:2012-01-01 00:00:00
abstract::Three-dimensional protein structures provide invaluable information for understanding and regulating biological functions of proteins. The GalaxyWEB server predicts protein structure from sequence by template-based modeling and refines loop or terminus regions by ab initio modeling. This web server is based on the met...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks493
更新日期:2012-07-01 00:00:00
abstract::Genomic DNA methylation contributes substantively to transcriptional regulations that underlie mammalian development and cellular differentiation. Much effort has been made to decipher the molecular mechanisms governing the establishment and maintenance of DNA methylation patterns. However, little is known about genom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr017
更新日期:2011-05-01 00:00:00
abstract::An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucle...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.8.1941
更新日期:1993-04-25 00:00:00
abstract::G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gky187
更新日期:2018-04-20 00:00:00
abstract::Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover causal mutations that confer desired phenotypic functions. ALE not only represents a controllable experimental approach to systematically discover genotype-phenotype relationships, but also allows for the revelation of the series o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky983
更新日期:2019-01-08 00:00:00
abstract::Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv608
更新日期:2015-08-18 00:00:00