MHCPEP--a database of MHC-binding peptides: update 1995.


:MHCPEP is a curated database comprising over 6000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains peptide sequence, MHC specificity and when available, experimental method, observed activity, binding affinity, source protein, anchor positions, as well as publication references. The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using Gopher, FTP or WWW.


Nucleic Acids Res


Nucleic acids research


Brusic V,Rudy G,Kyne AP,Harrison LC




Has Abstract


1996-01-01 00:00:00














  • Sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA.

    abstract::The sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA has been determined. The sequence contains the entire coat protein cistron as well as regions to its left and right. Sequence characterization was by conventional methods for use with uniformly 32P labeled RNA complemented by newer methods for ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Guilley H,Jonard G,Kukla B,Richards KE

    更新日期:1979-04-01 00:00:00

  • Efficient and risk-reduced genome editing using double nicks enhanced by bacterial recombination factors in multiple species.

    abstract::Site-specific DNA double-strand breaks have been used to generate knock-in through the homology-dependent or -independent pathway. However, low efficiency and accompanying negative impacts such as undesirable indels or tumorigenic potential remain problematic. In this study, we present an enhanced reduced-risk genome ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: He X,Chen W,Liu Z,Yu G,Chen Y,Cai YJ,Sun L,Xu W,Zhong L,Gao C,Chen J,Zhang M,Yang S,Yao Y,Zhang Z,Ma F,Zhang CC,Lu HP,Yu B,Cheng TL,Qiu J,Sheng Q,Zhou HM,Lv ZR,Yan J,Zhou Y,Qiu Z,Cui Z,Zhang X,Me

    更新日期:2020-06-04 00:00:00

  • Interaction of influenza virus NS1 protein and the human homologue of Staufen in vivo and in vitro.

    abstract::A screening for human proteins capable of interacting with influenza virus NS1 has been carried out using the two-hybrid genetic trap in yeast. A cDNA corresponding to the human homologue of Drosophila melanogaster Staufen protein (hStaufen) was isolated that fulfilled all genetic controls of the two-hybrid protocol. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Falcón AM,Fortes P,Marión RM,Beloso A,Ortín J

    更新日期:1999-06-01 00:00:00

  • Determinants of redox sensitivity in RsrA, a zinc-containing anti-sigma factor for regulating thiol oxidative stress response.

    abstract::Various environmental oxidative stresses are sensed by redox-sensitive regulators through cysteine thiol oxidation or modification. A few zinc-containing anti-sigma (ZAS) factors in actinomycetes have been reported to respond sensitively to thiol oxidation, among which RsrA from Streptomyces coelicolor is best charact...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jung YG,Cho YB,Kim MS,Yoo JS,Hong SH,Roe JH

    更新日期:2011-09-01 00:00:00

  • Base-stacking and base-pairing contributions into thermal stability of the DNA double helix.

    abstract::Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the fi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yakovchuk P,Protozanova E,Frank-Kamenetskii MD

    更新日期:2006-01-31 00:00:00

  • A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level.

    abstract::We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Walther J,Dans PD,Balaceanu A,Hospital A,Bayarri G,Orozco M

    更新日期:2020-03-18 00:00:00

  • The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors.

    abstract::In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seem...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rodríguez-Gil A,García-Martínez J,Pelechano V,Muñoz-Centeno Mde L,Geli V,Pérez-Ortín JE,Chávez S

    更新日期:2010-08-01 00:00:00

  • The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation.

    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


    authors: Wendte JM,Haag JR,Pontes OM,Singh J,Metcalf S,Pikaard CS

    更新日期:2019-09-26 00:00:00

  • Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli.

    abstract::Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hör J,Di Giorgio S,Gerovac M,Venturini E,Förstner KU,Vogel J

    更新日期:2020-09-18 00:00:00

  • DNA crosslinking and biological activity of a hairpin polyamide-chlorambucil conjugate.

    abstract::A prototype of a novel class of DNA alkylating agents, which combines the DNA crosslinking moiety chlorambucil (Chl) with a sequence-selective hairpin pyrrole-imidazole polyamide ImPy-beta-ImPy-gamma-ImPy-beta-Dp (polyamide 1), was evaluated for its ability to damage DNA and induce biological responses. Polyamide 1-Ch...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wang YD,Dziegielewski J,Wurtz NR,Dziegielewska B,Dervan PB,Beerman TA

    更新日期:2003-02-15 00:00:00

  • ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.

    abstract::It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf ( and ConSeq ( are two well-established web servers for calculating the evolutionar...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ashkenazy H,Erez E,Martz E,Pupko T,Ben-Tal N

    更新日期:2010-07-01 00:00:00

  • Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape.

    abstract::The σ subunit of bacterial RNA polymerase (RNAP) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of RNA synthesis, abortive initiation and promoter escape. The post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pupov D,Kuzin I,Bass I,Kulbachinskiy A

    更新日期:2014-04-01 00:00:00

  • Persistence of DNA synthesis arrest sites in the presence of T4 DNA polymerase and T4 gene 32, 44, 45 and 62 DNA polymerase accessory proteins.

    abstract::DNA synthesis by phage T4 DNA polymerase is arrested at specific sequences in single-stranded DNA templates. To determine whether or not T4 DNA polymerase accessory proteins 32, 44, 45 and 62 eliminated recognition of these arrest sites, unique primer-templates were constructed in which DNA synthesis began at a DNA pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Charette MF,Weaver DT,DePamphilis ML

    更新日期:1986-04-25 00:00:00

  • A simple method for N-15 labelling of exocyclic amino groups in synthetic oligodeoxynucleotides.

    abstract::The use of the ammonia deprotection step to introduce (15)N labels at specific exocyclic amino positions of adenine, cytosine, guanine or 2-aminopurine of oligodeoxynucleotides is described. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Acedo M,Fàbrega C,Aviño A,Goodman M,Fagan P,Wemmer D,Eritja R

    更新日期:1994-08-11 00:00:00

  • Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.

    abstract::IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Prieto AI,Kahramanoglou C,Ali RM,Fraser GM,Seshasayee AS,Luscombe NM

    更新日期:2012-04-01 00:00:00

  • Excision of 8-oxoguanine within clustered damage by the yeast OGG1 protein.

    abstract::Clustered damages are formed in DNA by ionising radiation and radiomimetic anticancer agents and are thought to be biologically severe. 7,8-dihydro-8-oxoguanine (8-oxoG), a major DNA damage resulting from oxidative attack, is highly mutagenic leading to a high level of G.C-->T.A transversions if not previously excised...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: David-Cordonnier MH,Boiteux S,O'Neill P

    更新日期:2001-03-01 00:00:00

  • Promoter selectivity of the stationary-phase forms of Escherichia coli RNA polymerase and conversion in vitro of the S1 form enzyme into a log-phase enzyme-like form.

    abstract::Upon growth transition of Escherichia coli cells from exponential to stationary phase, RNA polymerase is converted into at least three different forms (S1, S2 and S3), which could be separately isolated by phosphocellulose column chromatography (Ozaki et al., 1991 (2)). Here, the promoter selectivity of these three st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ozaki M,Fujita N,Wada A,Ishihama A

    更新日期:1992-01-25 00:00:00

  • A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy.

    abstract::DNA-damage response machinery is crucial to maintain the genomic integrity of cells, by enabling effective repair of even highly lethal lesions such as DNA double-strand breaks (DSBs). Defects in specific genes acquired through mutations, copy-number alterations or epigenetic changes can alter the balance of these pat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: Liu C,Srihari S,Cao KA,Chenevix-Trench G,Simpson PT,Ragan MA,Khanna KK

    更新日期:2014-06-01 00:00:00

  • NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors.

    abstract::Nucleosomes, a basic structural unit of eukaryotic chromatin, play a significant role in regulating gene expression. We have developed a web tool based on DNA sequences known from empirical and theoretical studies to influence DNA bending and flexibility, and to exclude nucleosomes. NXSensor (available at http://www.s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Luykx P,Bajić IV,Khuri S

    更新日期:2006-07-01 00:00:00

  • The sequence of the Drosophila melanogaster gene for yolk protein 1.

    abstract::We have determined the complete nucleotide sequence of the hormonally regulated yolk protein 1 (YP1) gene of Drosophila melanogaster. We have also determined the sequence location of the 5' and 3' ends of both the mature mRNA and the gene's only intron. The YP1 gene contains sequences similar to those found in many ot...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hung MC,Wensink PC

    更新日期:1981-12-11 00:00:00

  • Visualisation of extensive water ribbons and networks in a DNA minor-groove drug complex.

    abstract::The crystal structure is reported of a complex between an ethyl derivative of the minor-groove drug furamidine and the dodecanucleotide duplex d(CGCGAATTCGCG)2, which has been refined to 1.85 A resolution and an R factor of 16.6% for data collected at -173 degreesC. An exceptionally large number (220) of water molecul...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Guerri A,Simpson IJ,Neidle S

    更新日期:1998-06-15 00:00:00

  • DNA methylase from HeLa cell nuclei.

    abstract::A DNA methylase has been purified 270-fold from HeLa cell nuclei by chromatography on DEAE-cellulose, phosphocellulose, and hydroxyapatite. The enzyme transfers methyl groups from S-adenosyl-L-methionine to cytosine residues in DNA. The sole product of the reaction has been identified as 5-methylcytosine. The enzyme i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Roy PH,Weissbach A

    更新日期:1975-10-01 00:00:00

  • FBXL5-mediated degradation of single-stranded DNA-binding protein hSSB1 controls DNA damage response.

    abstract::Human single-strand (ss) DNA binding proteins 1 (hSSB1) has been shown to participate in DNA damage response and maintenance of genome stability by regulating the initiation of ATM-dependent signaling. ATM phosphorylates hSSB1 and prevents hSSB1 from ubiquitin-proteasome-mediated degradation. However, the E3 ligase th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chen ZW,Liu B,Tang NW,Xu YH,Ye XY,Li ZM,Niu XM,Shen SP,Lu S,Xu L

    更新日期:2014-10-01 00:00:00

  • AntigenDB: an immunoinformatics database of pathogen antigens.

    abstract::The continuing threat of infectious disease and future pandemics, coupled to the continuous increase of drug-resistant pathogens, makes the discovery of new and better vaccines imperative. For effective vaccine development, antigen discovery and validation is a prerequisite. The compilation of information concerning p...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ansari HR,Flower DR,Raghava GP

    更新日期:2010-01-01 00:00:00

  • Structure of recombinant rat UBF by electron image analysis and homology modelling.

    abstract::We have studied the structure of recombinant rat UBF (rrUBF), an RNA polymerase I transcription factor, by electron microscopy and image analysis of single particles contrasted with methylamine tungstate. Recombinant rat UBF appeared to be a flat, U-shaped protein with a central region of low density. In the dominant ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Neil KJ,Ridsdale RA,Rutherford B,Taylor L,Larson DE,Glibetic M,Rothblum LI,Harauz G

    更新日期:1996-04-15 00:00:00

  • The mouse and human homologs of DMC1, the yeast meiosis-specific homologous recombination gene, have a common unique form of exon-skipped transcript in meiosis.

    abstract::Genetic recombination in meiosis plays an important role in generating diversity of genetic information. In yeast an Escherichia coli RecA-like gene, DMC1, is expressed in meiotic prophase and its product co-localizes with Rad51 protein on zygotene chromosomes. We have cloned the mouse and human homologs of the yeast ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Habu T,Taki T,West A,Nishimune Y,Morita T

    更新日期:1996-02-01 00:00:00

  • Direct isolation of poly(A)+ RNA from 4 M guanidine thiocyanate-lysed cell extracts using locked nucleic acid-oligo(T) capture.

    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


    authors: Jacobsen N,Nielsen PS,Jeffares DC,Eriksen J,Ohlsson H,Arctander P,Kauppinen S

    更新日期:2004-04-19 00:00:00

  • Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon.

    abstract::Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we u...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ranganathan S,Bai G,Lyubetskaya A,Knapp GS,Peterson MW,Gazdik M,C Gomes AL,Galagan JE,McDonough KA

    更新日期:2016-01-08 00:00:00

  • Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution.

    abstract::Directed molecular evolution and combinatorial methodologies are playing an increasingly important role in the field of protein engineering. The general approach of generating a library of partially randomized genes, expressing the gene library to generate the proteins the library encodes and then screening the protei...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: Neylon C

    更新日期:2004-02-27 00:00:00

  • Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

    abstract::The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts the alignments of a number of genomes computed by our group, allowing ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Brudno M,Poliakov A,Minovitsky S,Ratnere I,Dubchak I

    更新日期:2007-07-01 00:00:00