Abstract:
:Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0 http://gnmdb.csb.pitt.edu/, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Li H,Chang YY,Yang LW,Bahar Idoi
10.1093/nar/gkv1236subject
Has Abstractpub_date
2016-01-04 00:00:00pages
D415-22issue
D1eissn
0305-1048issn
1362-4962pii
gkv1236journal_volume
44pub_type
杂志文章abstract::The advent of RNA-sequencing and microarray technologies has led to rapid growth of transcriptome data generated for a wide range of organisms, under various cellular, organ and individual conditions. Since the number of possible combinations of intercellular and extracellular conditions is almost unlimited, catalogin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1155
更新日期:2019-01-08 00:00:00
abstract::The 5' processing of rat pre-tRNA(Lys) and a series of mutant derivatives by rat cytosolic RNase P was examined. In standard, non-kinetic assays, mutant precursors synthesized in vitro with 5' leader sequences of 10, 17, 24, 25, and 46 nucleotides were processed to approximately equal levels and yielded precisely clea...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.16.3347
更新日期:1994-08-25 00:00:00
abstract::Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG isla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa556
更新日期:2020-09-04 00:00:00
abstract::A single locus in the mouse, rat and chicken encodes both alkali myosin light chains, MLC1F and MLC3F. This gene has two distinct promoters and gives rise to two different primary transcripts, which are processed by alternative and different modes of splicing to form MLC1F and MLC3F mRNAs. The MLC1F/MLC3F gene is very...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.13.4623
更新日期:1985-07-11 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::Chelation of divalent cations by 5 mM EDTA and subsequent removal by dialysis from a cytoplasmic HeLa cell extract leads to a complete loss of 5S rRNA transcription without affecting tRNA synthesis. Transcription complexes for 5S RNA can no longer be assembled in such a zinc-depleted extract and this ability can be fu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.23.8971
更新日期:1984-12-11 00:00:00
abstract::Extensive research has characterized distinct exogenous RNAi pathways interfering in gene expression during vegetative growth of the unicellular model ciliate Paramecium. However, role of RNAi in endogenous transcriptome regulation, and environmental adaptation is unknown. Here, we describe the first genome-wide profi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz553
更新日期:2019-09-05 00:00:00
abstract::Oxanine (O) is a deamination product derived from guanine with the nitrogen at the N1 position substituted by oxygen. Cytosine, thymine, adenine, guanine as well as oxanine itself can be incorporated by Klenow Fragment to pair with oxanine in a DNA template with similar efficiency, indicating that oxanine in DNA may c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh747
更新日期:2004-08-02 00:00:00
abstract::WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). WorfDB serves as a central ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg092
更新日期:2003-01-01 00:00:00
abstract::Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buff...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx553
更新日期:2017-09-06 00:00:00
abstract::iSARST is a web server for efficient protein structural similarity searches. It is a multi-processor, batch-processing and integrated implementation of several structural comparison tools and two database searching methods: SARST for common structural homologs and CPSARST for homologs with circular permutations. iSARS...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp291
更新日期:2009-07-01 00:00:00
abstract::Non-coding RNAs (ncRNAs) have diverse essential biological functions in all organisms, and in eukaryotes, two such classes of ncRNAs are the small nucleolar (sno) and small nuclear (sn) RNAs. In this study, we have identified and characterized a collection of sno and snRNAs in Giardia lamblia, by exploiting our discov...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks887
更新日期:2012-11-01 00:00:00
abstract::Engineered derivatives of Autographa californica multiple nucleocapsid nuclear polyhedrosis virus (AcMNPV) possessing a unique restriction site provide a source of viral DNA that can be linearized by digestion with a specific endonuclease. Circular or linearized DNA from two such viruses were compared in terms of thei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.19.5667
更新日期:1990-10-11 00:00:00
abstract::In eukaryotic ribosome, the N domain of polypeptide release factor eRF1 is involved in decoding stop signals in mRNAs. However, structure of the decoding site remains obscure. Here, we specifically altered the stop codon recognition pattern of human eRF1 by point mutagenesis of the invariant Glu55 and Tyr125 residues ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki927
更新日期:2005-11-10 00:00:00
abstract::In plants, nuclear multisubunit RNA polymerases IV and V are RNA Polymerase II-related enzymes that synthesize non-coding RNAs for RNA-directed DNA methylation (RdDM) and transcriptional gene silencing. Here, we tested the importance of the C-terminal domain (CTD) of Pol IV's largest subunit given that the Pol II CTD ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz615
更新日期:2019-09-26 00:00:00
abstract::Messenger RNA in eukaryotes is comprised of several abundance classes. Also, the decay of these unstable molecules shows at least two very different lifetimes. Two independent techniques are used here to examine the relation between message abundance and lifetime in cell lines from very different organisms. The method...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.3057
更新日期:1978-08-01 00:00:00
abstract::The DNA-Actinomycin D interaction has been studied by resonance Raman effect using DNA as chromophore. First, the resonance Raman spectra of DNA obtained with a U.V. excitation at wavelengths of 300 nm and 280 nm are presented. The main Raman hands are assigned to the convenient nucleic bases by comparison with the sp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.2969
更新日期:1978-08-01 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::The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42,574 serine, threoni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1104
更新日期:2011-01-01 00:00:00
abstract::We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq275
更新日期:2010-07-01 00:00:00
abstract::Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw162
更新日期:2016-04-20 00:00:00
abstract::Previous studies of the epithelial specificity of the human papillomavirus type 16 (HPV-16) enhancer pointed out an important role of nuclear factor I (NFI). In epithelial cells, NFI proteins are derived from the NFI-C gene and referred to as NFI/CTF. In contrast, fibroblasts, where the enhancer is inactive, express h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.19.3825
更新日期:1994-09-25 00:00:00
abstract::The presence of the C.C mispair in a defined duplex oligodeoxynucleotide enhanced its capacity to serve as a substrate for highly purified human DNA methyltransferase. Analysis of tritiated reaction products showed that the C.C mispair acted as a "methylation acceptor" in that it was itself rapidly methylated. The m5C...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.17.6899
更新日期:1987-09-11 00:00:00
abstract::In vitro compartmentalization (IVC) was employed for the first time to select for novel bacteriophage lambda integrase variants displaying significantly enhanced recombination activity on a non-cognate target DNA sequence. These variants displayed up to 9-fold increased recombination activity over the parental enzyme,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1089
更新日期:2010-03-01 00:00:00
abstract::We have isolated and characterized DNA probes that detect homologies between the X and Y chromosomes. Clone St25 is derived from the q13-q22 region of the X chromosome and recognizes a 98% homologous sequence on the Y chromosome. Y specific fragments were present in DNAs from 5 Yq-individuals and from 4 out of 7 XX ma...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.15.5485
更新日期:1985-08-12 00:00:00
abstract::The expression of the nicotinic acetylcholine receptor alpha 2 subunit gene is highly restricted to the Spiriform lateralis nucleus of the Chick diencephalon. As a first step toward understanding the molecular mechanism underlying this regulation, we have investigated the structural and regulatory properties of the 5'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.9.2185
更新日期:1993-05-11 00:00:00
abstract::The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nasce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx318
更新日期:2017-07-27 00:00:00
abstract::In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utili...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj158
更新日期:2006-01-01 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::Treatment of cells with DNA damaging agents leads to induction of a variety of genes involved in different cellular processes. We have applied a lacZ-based gene trap strategy to search for new mammalian genes induced by genotoxic stress. A population of 32 x 10(3) neo r clones stably transfected with a gene trap vecto...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.23.4803
更新日期:1997-12-01 00:00:00