Abstract:
:R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Vanquelef E,Simon S,Marquant G,Garcia E,Klimerak G,Delepine JC,Cieplak P,Dupradeau FYdoi
10.1093/nar/gkr288subject
Has Abstractpub_date
2011-07-01 00:00:00pages
W511-7issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkr288journal_volume
39pub_type
杂志文章abstract::OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1238
更新日期:2011-01-01 00:00:00
abstract::How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2019-06-20 00:00:00
abstract::The prime mechanism by which p53 acts as a tumor suppressor is as a transcription factor regulating the expression of diverse downstream genes. The DNA-binding domain of p53 (p53DBD) interacts with defined DNA sites and is the main target for mutations in human primary tumors. Here, we show that the CWWG motif, found ...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkq1044
更新日期:2011-03-01 00:00:00
abstract::Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage 29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base ...
journal_title:Nucleic acids research
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doi:10.1093/nar/gks724
更新日期:2012-10-01 00:00:00
abstract::A gene bank of Staphylococcus aureus strain Cowan I was established using an E. coli HB101/pBR327 host-vector system. Recombinants expressing staphylococcal protein A (SPA) were detected using an IgG-binding assay. A 3.2 Kb DNA fragment directing the synthesis of SPA in E. coli was identified. SPA produced by E. coli ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.10.3065
更新日期:1983-05-25 00:00:00
abstract::Interactions between proteins bound to distant sites along a DNA molecule require bending and twisting deformations in the intervening DNA. In certain systems, the sterically allowed protein-DNA and protein-protein interactions are hypothesized to produce loops with distinct geometries that may also be thermodynamical...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkn389
更新日期:2008-07-01 00:00:00
abstract::The HpaR-mediated regulation of the hpa-meta operon (Pg promoter) of the 4-hydroxyphenylacetic acid catabolic pathway of Escherichia coli has been studied. The HpaR regulator was purified to homogeneity showing that it is able to bind selectively to 4-hydroxyphenylacetic, 3-hydroxyphenylacetic and 3,4-dihydroxyphenyla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg851
更新日期:2003-11-15 00:00:00
abstract::Biological evolution resulted in a homochiral world in which nucleic acids consist exclusively of d-nucleotides and proteins made by ribosomal translation of l-amino acids. From the perspective of synthetic biology, however, particularly anabolic enzymes that could build the mirror-image counterparts of biological mac...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkx079
更新日期:2017-04-20 00:00:00
abstract::Smad proteins transduce signals from transforming growth factor-beta (TGF-beta) receptors and regulate transcription of target genes. TGF-beta is implicated in the regulation of the smooth muscle cell specific gene SM22alpha, but little is known about how Smads are involved in SM22alpha gene transcription. In this rep...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2003-02-15 00:00:00
abstract::Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits t...
journal_title:Nucleic acids research
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更新日期:1995-06-25 00:00:00
abstract::The -175 T greater than C mutation in the promoter of the A gamma- or G gamma-globin gene causes a 50-100 fold increase of the expression of the respective gene in adult erythroid cells (Hereditary Persistence of Fetal Hemoglobin). We show here that this mutation increases 3-9 fold the expression of a gamma-CAT report...
journal_title:Nucleic acids research
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更新日期:1989-07-25 00:00:00
abstract::Cell specific expression of the insulin gene is achieved through transcriptional mechanisms operating on 5' flanking DNA elements. In the enhancer of rat I insulin gene, two elements, the Nir and Far boxes, located at positions -104 and -233 respectively and containing the same octameric motif are essential for B cell...
journal_title:Nucleic acids research
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doi:10.1093/nar/21.7.1595
更新日期:1993-04-11 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::We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl144
更新日期:2006-04-13 00:00:00
abstract::Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia col...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1234
更新日期:2021-01-25 00:00:00
abstract::Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the uniq...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkt1237
更新日期:2014-02-01 00:00:00
abstract::We have previously shown that integration of a polyoma vector containing rodent repetitive elements into rat cellular DNA is non-random (Wallenburg et al. J. Virol. 50: 678-683). Junctions between the polyoma vector and the host DNA occur in the repetitive sequences of the vector about ten times more frequently than w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.19.7849
更新日期:1987-10-12 00:00:00
abstract::The advent of jellyfish green fluorescent protein and its spectral variants, together with promising new fluorescent proteins from other classes of the Cnidarian phylum (coral and anemones), has greatly enhanced and promises to further boost the detection and localization of proteins in cell biology. It has been less ...
journal_title:Nucleic acids research
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doi:10.1093/nar/29.5.1013
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abstract::The sequence of a DNA fragment about 1 Kbp long located at the 3' boundary of the chicken alpha globin gene domain, including the 3'-side matrix attachment point and the site of transcription termination, was determined. It contains a repetitive DNA element and the AT-rich (easily denaturable) DNA segment conserved at...
journal_title:Nucleic acids research
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abstract::Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from many phyla. Pnkp is composed of three catalytic modules: an N-terminal polynucleotide 5' kinase, a central 2',3' phosphatase and a C-terminal ligase. The phosphatase module is a Mn(2+)-dependent phosphodiesterase...
journal_title:Nucleic acids research
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abstract::By using a synthetic DNA probe derived from an amino acid sequence in the most conserved region of three known photolyases (Escherichia coli, Anacystis nidulans and Saccharomyces cerevisiae), we isolated a DNA fragment containing two long open reading frames (ORFs) from a genomic DNA library of Streptomyces griseus. O...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks661
更新日期:2012-10-01 00:00:00
abstract::Members of the basic helix-loop-helix (bHLH) family of transcription factors regulate a wide array of developmental processes in many cell types, including cell fate specification, differentiation and morphogenesis. Our studies describe the cloning of a gene from the nematode Caenorhabditis elegans that is closely rel...
journal_title:Nucleic acids research
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doi:10.1093/nar/29.21.4423
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abstract::Transcriptional regulation of the delta-aminolevulinic acid synthetase gene of Rhizobium meliloti was investigated under conditions of normal vegetative growth and during symbiosis with the legume host alfalfa. S1 nuclease mapping and DNA sequence analysis indicated that transcription originates from two sites separat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.16.5965
更新日期:1985-08-26 00:00:00
abstract::The archaeal and eukaryotic evolutionary domains diverged from each other approximately 2 billion years ago, but many of the core components of their transcriptional and translational machineries still display a readily recognizable degree of similarity in their primary structures. The F and P subunits present in arch...
journal_title:Nucleic acids research
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doi:10.1093/nar/28.21.4299
更新日期:2000-11-01 00:00:00
abstract::DNA fragments containing mispaired and modified bases, bulges, lesions and specific sequences have altered conformation. Methods for separating complex samples of DNA fragments based on conformation but independent of length have many applications, including (i) separation of mismatched or unmatched DNA fragments from...
journal_title:Nucleic acids research
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doi:10.1093/nar/gnh018
更新日期:2004-02-03 00:00:00
abstract::A class II site-specific endodeoxyribonuclease (SalPI) was identified in cell-free extracts of Streptomyces albus CMI 52766 after high speed centrifugation and fractionation through Bio Gel AO.5M. SalPI cleaves lambda DNA into at least 18 fragments. Five cleavage sites were located in the linear lambda map by the use ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.6.1989
更新日期:1977-06-01 00:00:00
abstract::The human embryonal carcinoma cell line NEC14 can be induced to differentiate by the addition of 10(-2)M N,N'-hexamethylene-bis-acetamide (HMBA). A subtractive cDNA library specific to undifferentiated NEC14 cells was constructed using oligo(dT)30-Latex and polymerase chain reaction (PCR). The method was designed to i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.25.7097
更新日期:1991-12-01 00:00:00
abstract::IL-2 gene expression in activated T-cells is initiated by chromatin remodeling at the IL-2 proximal promoter and conversion of a transcriptional repressor into a potent transcriptional activator. A purine-box regulator complex was purified from activated Jurkat T-cell nuclei based on sequence-specific DNA binding to t...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkm117
更新日期:2007-01-01 00:00:00