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：:Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa663
更新日期：2020-09-25 00:00:00
abstract：:DNA non-homologous end joining, the major mechanism for the repair of DNA double-strands breaks (DSB) in mammalian cells requires the DNA-dependent protein kinase (DNA-PK), a complex composed of a large catalytic subunit of 460 kDa (DNA-PKcs) and the heterodimer Ku70-Ku80 that binds to double-stranded DNA ends. Mutati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.23.4778
更新日期：2000-12-01 00:00:00
abstract：:Abasic sites (AP-sites) are frequent DNA lesions, arising by spontaneous base hydrolysis or as intermediates of base excision repair (BER). The hemiacetal at the anomeric centre renders them chemically reactive, which presents a challenge to biochemical and structural investigation. Chemically more stable AP-site anal...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1520
更新日期：2016-03-18 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：:The thyroid hormone receptor alpha (THRA or c-erbA-1) gene belongs to a family of genes which encode nuclear receptors for various hydrophobic ligands such as steroids, vitamin D, retinoic acid and thyroid hormones. These receptors are composed of several domains important for hormone-binding, DNA-binding, dimerizatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.5.1105
更新日期：1991-03-11 00:00:00
abstract：:Approximately 30% of human tumors characterized to date express DNA polymerase beta (pol beta) variant proteins. Two of the polymerase beta cancer-associated variants are sequence-specific mutators, and one of them binds to DNA but has no polymerase activity. The Leu22Pro (L22P) DNA polymerase beta variant was identif...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1053
更新日期：2008-02-01 00:00:00
abstract：:The remarkable selectivity of N-methyl mesoporphyrin IX (NMM) for G-quadruplexes (GQs) is long known, however its ability to stabilize and bind GQs has not been investigated in detail. Through the use of circular dichroism, UV-visible spectroscopy and fluorescence resonance energy transfer (FRET) melting assay we have...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks152
更新日期：2012-07-01 00:00:00
abstract：:The formation of interstrand cross-links in nucleic acids can have a strong impact on biological function of nucleic acids; therefore, many cross-linking agents have been developed for biological applications. Despite numerous studies, there remains a need for cross-linking agents that exhibit both efficiency and sele...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt197
更新日期：2013-07-01 00:00:00
abstract：:Methionyl-tRNA synthetase belongs to the class I aminoacyl-tRNA synthetase family characterized both by a catalytic center built around a Rossmann Fold and by the presence of the two peptidic marker sequences HIGH and KMSKS. In this study, the role of the 21HLGH24 motif of Escherichia coli methionyl-tRNA synthetase wa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.23.4793
更新日期：1995-12-11 00:00:00
abstract：:Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv903
更新日期：2016-01-29 00:00:00
abstract：:Soil salinity is a significant threat to sustainable agricultural production worldwide. Plants must adjust their developmental and physiological processes to cope with salt stress. Although the capacity for adaptation ultimately depends on the genome, the exceptional versatility in gene regulation provided by the spli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1229
更新日期：2018-02-28 00:00:00
abstract：:Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw077
更新日期：2016-04-20 00:00:00
abstract：:The Homeodomain Resource is a comprehensive collection of sequence, structure and genomic information on the homeodomain protein family. Available through the Resource are both full-length and domain-only sequence data, as well as X-ray and NMR structural data for proteins and protein-DNA complexes. Also available is ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.1.336
更新日期：1999-01-01 00:00:00
abstract：:Heteroduplexes between the viral DNA of phiX174 and DNA from the replicative form (RF) of phage G4 were examined by electron microscopy. The single Eco RI site of G4-RF was utilized as a physical marker by preparing the heteroduplexes from the denatured, linear DNA obtained by restricting G4-RF with Eco RI endonucleas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.5.1979
更新日期：1979-01-01 00:00:00
abstract：:Potential pathways that could account for observed rapid rates of transcription reinitiation were explored. A nuclear extract system was established in which reinitiation rates were observed to be kinetically facilitated and in which the rate was sensitive to TATA box mutation. Kinetic facilitation of functional compl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.3.831
更新日期：1999-02-01 00:00:00
abstract：:A mass spectral method is described for the detection and identification of unusual nucleotide residues present in DNAs. Analysis by this method of intact, underivatized DNA from salmon sperm, calf thymus, mouse L-cells, wheat germ, M. lysodeikticus, E. Coli, and the bacteriophages 0X-174, fd, and lamda, yields diagno...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.11.2959
更新日期：1976-11-01 00:00:00
abstract：:The x-ray crystal structures of two new anti-HIV compounds, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine (2'-F-dd-araA) and 9-(2,3-dideoxy-2-fluoro-beta-D-threo- pentofuranosyl)hypoxanthine (2'-F-dd-aral), have been determined at two temperatures. Both crystals are in the space group P2(1)2(1)2(1), and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.459
更新日期：1992-02-11 00:00:00
abstract：:A circular trans-acting ribozyme designed to adopt the motif of the hepatitis delta virus (HDV) trans-acting ribozyme was produced. The circular form was generated in vitro by splicing a modified group I intron precursor RNA in which the relative order of the 5' and 3' splice sites, flanking the single HDV-like ribozy...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.18.4253
更新日期：1993-09-11 00:00:00
abstract：:Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.13.5125
更新日期：1986-07-11 00:00:00
abstract：:We report here spectroscopic and biochemical data of a novel series of sugar-modified oligodeoxy-nucleotides, the carbocyclic oligothymidylates, c(dT)3-20. In c(dT)n a methylene group has been substituted for the oxygen atom of the deoxyribose ring of the natural thymidylate unit. c(dT)10-20 form helical structures, i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.8.2133
更新日期：1990-04-25 00:00:00
abstract：:The genes encoding the RNA subunit of ribonuclease P from the unicellular cyanobacterium Synechocystis sp. PCC 6803, and from the heterocyst-forming strains Anabaena sp. PCC 7120 and Calothrix sp. PCC 7601 were cloned using the homologous gene from Anacystis nidulans (Synechococcus sp. PCC 6301) as a probe. The genes ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.23.6331
更新日期：1992-12-11 00:00:00
abstract：:The essential and universal N(6)-threonylcarbamoyladenosine (t(6)A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (Tsa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1397
更新日期：2015-02-18 00:00:00
abstract：:Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3' bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome v...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1525
更新日期：2016-05-05 00:00:00
abstract：:Infection of cultured cells with herpes simplex virus (HSV) results in the transcriptional induction of a small number of cellular genes. Although the majority of such genes are dependent upon viral protein synthesis for their induction, a small minority are not. These genes are induced by events occurring prior to th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.23.9261
更新日期：1986-12-09 00:00:00
abstract：:Light is a major external factor in regulating seed germination. Photoreceptor phytochrome B (PHYB) plays a predominant role in promoting seed germination in the initial phase after imbibition, partially by repressing phytochrome-interacting factor1 (PIF1). However, the mechanism underlying the PHYB-PIF1-mediated tran...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx283
更新日期：2017-07-07 00:00:00
abstract：:Minigenes encoding the peptide Met-Arg-Arg have been used to study the mechanism of toxicity of AGA codons proximal to the start codon or prior to the termination codon in bacteria. The codon sequences of the 'mini-ORFs' employed were initiator, combinations of AGA and CGA, and terminator. Both, AGA and CGA are low-us...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh784
更新日期：2004-08-18 00:00:00
abstract：:Over the past 10 years, fluorescent end-labeling of DNA fragments has evolved into the preferred method of DNA detection for a wide variety of applications, including DNA sequencing and PCR fragment analysis. One of the advantages inherent in fluorescent detection methods is the ability to perform multi-color analyses...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.11.2797
更新日期：1998-06-01 00:00:00
abstract：:The spatio-temporal organization of chromatin in the eukaryotic cell nucleus is of vital importance for transcription, DNA replication and genome maintenance. Each of these activities is tightly regulated in both time and space. While we have a good understanding of chromatin organization in space, for example in fixe...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkaa135
更新日期：2020-04-17 00:00:00
abstract：:Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better perfo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1141
更新日期：2014-02-01 00:00:00
abstract：:This paper describes the sequence of 257 nucleotides from the 3' end of RNA 2 of barley stripe mosaic virus ( BSMV , strain Argentina Mild) including an internal oligo (A) tract localized at a distance of 236 nucleotides from the 3' end, and the 3' terminal tRNA-like structure accepting tyrosine. This sequence is show...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.9.4001
更新日期：1984-05-11 00:00:00
