Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm.


:A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that are bound by the antibody with high affinity. This set of peptides is regarded as mimicking the genuine epitope of the antibody's interacting antigen and can be used to define it. Here we present PepSurf, an algorithm for mapping a set of affinity-selected peptides onto the solved structure of the antigen. The problem of epitope mapping is converted into the task of aligning a set of query peptides to a graph representing the surface of the antigen. The best match of each peptide is found by aligning it against virtually all possible paths in the graph. Following a clustering step, which combines the most significant matches, a predicted epitope is inferred. We show that PepSurf accurately predicts the epitope in four cases for which the epitope is known from a solved antibody-antigen co-crystal complex. We further examine the capabilities of PepSurf for predicting other types of protein-protein interfaces. The performance of PepSurf is compared to other available epitope mapping programs.


Nucleic Acids Res


Nucleic acids research


Mayrose I,Shlomi T,Rubinstein ND,Gershoni JM,Ruppin E,Sharan R,Pupko T




Has Abstract


2007-01-01 00:00:00














  • Engineering a portable riboswitch-LacP hybrid device for two-way gene regulation.

    abstract::Riboswitches are RNA-based regulatory devices that mediate ligand-dependent control of gene expression. However, there has been limited success in rationally designing riboswitches. Moreover, most previous riboswitches are confined to a particular gene and only perform one-way regulation. Here, we used a library scree...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jin Y,Huang JD

    更新日期:2011-10-01 00:00:00

  • Highly conserved sequences in the 3' untranslated region of mRNAs coding for homologous proteins in distantly related species.

    abstract::Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yaffe D,Nudel U,Mayer Y,Neuman S

    更新日期:1985-05-24 00:00:00

  • High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

    abstract::Understanding networks of protein-protein interactions constitutes an essential component on a path towards comprehensive description of cell function. Whereas efficient techniques are readily available for the initial identification of interacting protein partners, practical strategies are lacking for the subsequent ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pajunen M,Turakainen H,Poussu E,Peränen J,Vihinen M,Savilahti H

    更新日期:2007-01-01 00:00:00

  • HeLa DNA polymerase alpha activity in vitro: specific stimulation by a non-enzymic protein factor.

    abstract::A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Novak B,Baril EF

    更新日期:1978-01-01 00:00:00

  • Controlled loading of oligodeoxyribonucleotide monolayers onto unoxidized crystalline silicon; fluorescence-based determination of the surface coverage and of the hybridization efficiency; parallel imaging of the process by Atomic Force Microscopy.

    abstract::Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the inciden...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Cattaruzza F,Cricenti A,Flamini A,Girasole M,Longo G,Prosperi T,Andreano G,Cellai L,Chirivino E

    更新日期:2006-02-28 00:00:00

  • DNA replication in Physarum polycephalum: characterization of DNA replication products made in vivo in the presence of cycloheximide in strains sensitive and resistant to cycloheximide.

    abstract::Synchronous plasmodia of cycloheximide-sensitive and cycloheximide-resistant strains of Physarum polycephalum were labelled with 3[H]-deoxyadenosine in pulse and pulse-chase experiments in presence and absence of cycloheximide. The replication products were studied with alkaline sucrose gradient sedimentation analysis...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Funderud S,Haugli F

    更新日期:1977-02-01 00:00:00

  • Differences in unwinding of supercoiled DNA induced by the two enantiomers of anti-benzo[a]pyrene diol epoxide.

    abstract::The unwinding of supercoiled phi X174 RFI DNA induced by the tumorigenic (+) and non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) has been investigated by agarose slab-gel and ethidium titration tube gel electrophoresis. The differences in adduct conformat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Xu R,Birke S,Carberry SE,Geacintov NE,Swenberg CE,Harvey RG

    更新日期:1992-12-11 00:00:00

  • Femtosecond near-infrared laser microirradiation reveals a crucial role for PARP signaling on factor assemblies at DNA damage sites.

    abstract::Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Saquilabon Cruz GM,Kong X,Silva BA,Khatibzadeh N,Thai R,Berns MW,Yokomori K

    更新日期:2016-02-18 00:00:00

  • Conserved 5' flank homologies in dipteran 5S RNA genes that would function on 'A' form DNA.

    abstract::We have sequenced the 480 base pair (bp) repeating unit of the 5S RNA genes of the Dipteran fly Calliphora erythrocephala and compared this sequence to the three known 5S RNA gene sequences from the Dipteran Genus Drosophila (1,2). A striking series of five perfectly conserved homologies identically positioned within ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rubacha A,Sumner W 3rd,Richter L,Beckingham K

    更新日期:1984-11-12 00:00:00

  • Inferring the functional effect of gene expression changes in signaling pathways.

    abstract::Signaling pathways constitute a valuable source of information that allows interpreting the way in which alterations in gene activities affect to particular cell functionalities. There are web tools available that allow viewing and editing pathways, as well as representing experimental data on them. However, few metho...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sebastián-León P,Carbonell J,Salavert F,Sanchez R,Medina I,Dopazo J

    更新日期:2013-07-01 00:00:00

  • Site-specific modification of the lactose operator with acetylaminofluorene.

    abstract::We have synthesized the tetradecamer GAGCXGATAACAAG containing a part of the sequence of the lactose operator. A guanine base in the sequence is replaced by the adduct of the carcinogen 2-acetylaminofluorene with guanine. Under the standard conditions of de-protection, the fluorene moiety is lost, leaving behind a gua...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Stöhrer G,Osband JA,Alvarado-Urbina G

    更新日期:1983-08-11 00:00:00

  • Partitioning of zinc and copper within subnuclear nucleoprotein particles.

    abstract::Nuclei from frozen calf thymus suspended in buffer were analyzed for metal content prior to and after repeated washing. After three such extractions about 0.1 micrograms Zn/mg DNA and 0.025 micrograms Cu/mg DNA remained tightly associated with chromatin. This level of metal was essentially unchanged with subsequent wa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bryan SE,Vizard DL,Beary DA,LaBiche RA,Hardy KJ

    更新日期:1981-11-11 00:00:00

  • Genome engineering of isogenic human ES cells to model autism disorders.

    abstract::Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic suc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Martinez RA,Stein JL,Krostag AR,Nelson AM,Marken JS,Menon V,May RC,Yao Z,Kaykas A,Geschwind DH,Grimley JS

    更新日期:2015-05-26 00:00:00

  • Complete nucleotide sequence of a cloned chicken alpha-globin cDNA.

    abstract::Chicken globin double-stranded cDNA was synthesised from anaemic adult reticulocyte alpha- and beta-globin mRNA and ligated into the Hind III site of pBR322 using synthetic Hind III decamers. Transformation of E. coli x1776 resulted in the production of a number of alpha- and beta-cDNA clones. One of the alpha-type cl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Deacon NJ,Shine J,Naora H

    更新日期:1980-03-25 00:00:00

  • The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats.

    abstract::The potent anticancer drug actinomycin D (ActD) functions by intercalating into DNA at GpC sites, thereby interrupting essential biological processes including replication and transcription. Certain neurological diseases are correlated with the expansion of (CGG)n trinucleotide sequences, which contain many contiguous...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lo YS,Tseng WH,Chuang CY,Hou MH

    更新日期:2013-04-01 00:00:00

  • Spermine-DNA complexes build up metastable structures. Small-angle X-ray scattering and circular dichroism studies.

    abstract::Spermine-DNA complexes have been examined by small-angle and wide-angle X-ray scattering as well as by circular dichroism studies. Condensed complexes are building up below a critical ionic strength. We have found that at one and the same ionic strength condensed complexes having two different supramolecular structure...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Becker M,Misselwitz R,Damaschun H,Damaschun G,Zirwer D

    更新日期:1979-11-10 00:00:00

  • The BCL2 gene is regulated by a special AT-rich sequence binding protein 1-mediated long range chromosomal interaction between the promoter and the distal element located within the 3'-UTR.

    abstract::The 279-bp major breakpoint region (mbr) within the 3'-untranslated region (3'-UTR) of the BCL2 gene is a binding site of special AT-rich sequence binding protein 1 (SATB1) that is well known to participate in the long-range regulation of gene transcription. Our previous studies have revealed that the mbr could regula...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gong F,Sun L,Wang Z,Shi J,Li W,Wang S,Han X,Sun Y

    更新日期:2011-06-01 00:00:00

  • Spacer-length dependence of programmed -1 or -2 ribosomal frameshifting on a U6A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting.

    abstract::Programmed -1 ribosomal frameshifting is employed in the expression of a number of viral and cellular genes. In this process, the ribosome slips backwards by a single nucleotide and continues translation of an overlapping reading frame, generating a fusion protein. Frameshifting signals comprise a heptanucleotide slip...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lin Z,Gilbert RJ,Brierley I

    更新日期:2012-09-01 00:00:00

  • Molecular determinants of the DprA-RecA interaction for nucleation on ssDNA.

    abstract::Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its lo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lisboa J,Andreani J,Sanchez D,Boudes M,Collinet B,Liger D,van Tilbeurgh H,Guérois R,Quevillon-Cheruel S

    更新日期:2014-06-01 00:00:00

  • 14-3-3tau associates with and activates the MEF2D transcription factor during muscle cell differentiation.

    abstract::Myocyte enhancer binding factor 2 (MEF2) proteins belong to the MADS box family of transcription factors and four MEF2 proteins, MEF2A, MEF2B, MEF2C and MEF2D, have been found. MEF2 proteins have been shown to play critical roles in differentiation of muscles and neuronal tissues. How transactivational activity of MEF...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Choi SJ,Park SY,Han TH

    更新日期:2001-07-01 00:00:00

  • Rational design and PCR-based synthesis of an artificial Schizophyllum commune xylanase gene.

    abstract::A synthetic gene encoding the Schizophyllum commune xylanase XynA was constructed by a novel PCR-based procedure. Three long oligonucleotides were synthesized and used in combination with flanking PCR primers to generate a 607 base pair gene which contained 31 unique locations for restriction enzyme cleavage. The amin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Graham RW,Atkinson T,Kilburn DG,Miller RC Jr,Warren RA

    更新日期:1993-10-25 00:00:00

  • Identification of the ATP-binding site in the terminase subunit pUL56 of human cytomegalovirus.

    abstract::Human cytomegalovirus (HCMV) terminase is composed of subunits pUL56 (130 kDa) and pUL89 ( approximately 75 kDa), encoded by the UL56 and UL89 genes. In a recent investigation, we demonstrated that the main ATPase activity is associated with the large terminase subunit pUL56. The protein has two putative ATP-binding s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Scholz B,Rechter S,Drach JC,Townsend LB,Bogner E

    更新日期:2003-03-01 00:00:00

  • End-bridging is required for pol mu to efficiently promote repair of noncomplementary ends by nonhomologous end joining.

    abstract::DNA polymerase mu is a member of the mammalian pol X family and reduces deletion during chromosome break repair by nonhomologous end joining (NHEJ). This biological role is linked to pol mu's ability to promote NHEJ of ends with noncomplementary 3' overhangs, but questions remain regarding how it performs this role. W...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Davis BJ,Havener JM,Ramsden DA

    更新日期:2008-05-01 00:00:00

  • CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens.

    abstract::The potency of the immune response has still to be harnessed effectively to combat human cancers. However, the discovery of T-cell targets in melanomas and other tumors has raised the possibility that cancer vaccines can be used to induce a therapeutically effective immune response against cancer. The targets, cancer-...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Almeida LG,Sakabe NJ,deOliveira AR,Silva MC,Mundstein AS,Cohen T,Chen YT,Chua R,Gurung S,Gnjatic S,Jungbluth AA,Caballero OL,Bairoch A,Kiesler E,White SL,Simpson AJ,Old LJ,Camargo AA,Vasconcelos AT

    更新日期:2009-01-01 00:00:00

  • Nucleosome positioning as a critical determinant for the DNA cleavage sites of mammalian DNA topoisomerase II in reconstituted simian virus 40 chromatin.

    abstract::We have assessed the ability of nucleosomes to influence the formation of mammalian topoisomerase II-DNA complexes by mapping the sites of cleavage induced by four unrelated topoisomerase II inhibitors in naked versus nucleosome-reconstituted SV40 DNA. DNA fragments were reconstituted with histone octamers from HeLa c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Capranico G,Jaxel C,Roberge M,Kohn KW,Pommier Y

    更新日期:1990-08-11 00:00:00

  • Structural repeat units of Chinese hamster ovary chromatin. Evidence for variations in repeat unit DNA size in higher eukaryotes.

    abstract::DNA lengths in the structural repeat units of Chinese hamster ovary (CHO) and chicken erythrocyte chromatin were compared by analyzing the sizes of DNA fragments produced after treatment of nuclei with staphylococcal nuclease. The repeat length of CHO chromatin (173 +- 4 BP) is about 20 base pairs (BP) smaller than th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rill RL,Nelson DA,Oosterhof DK,Hozier JC

    更新日期:1977-04-01 00:00:00

  • A short 5' region of the long terminal repeat is required for regulation by hormone and heat shock of Drosophila retrotransposon 1731.

    abstract::1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or de...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ziarczyk P,Best-Belpomme M

    更新日期:1991-10-25 00:00:00

  • Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference.

    abstract::Few transcriptional regulatory networks have been described in non-model organisms. In Entamoeba histolytica seminal aspects of pathogenesis are transcriptionally controlled, however, little is known about transcriptional regulatory networks that effect gene expression in this parasite. We used expression data from tw...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hackney JA,Ehrenkaufer GM,Singh U

    更新日期:2007-01-01 00:00:00

  • Two closely spaced promoters are equally activated by a remote enhancer: evidence against a scanning model for enhancer action.

    abstract::To explain the activation of transcription by a remote enhancer, two models are most often considered, namely looping and scanning. A scanning model, also referred to as 'polymerase entry site' model predicts that for two adjacent promoters the one proximal to an enhancer would be preferentially activated. Preferentia...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Heuchel R,Matthias P,Schaffner W

    更新日期:1989-11-25 00:00:00

  • Studies on the mechanism of DNA cleavage by ethidium.

    abstract::Ethidium causes the cleavage of DNA via a light and oxygen dependent process. Using covalently closed circular DNA as a substrate, the saturation kinetics and the dependence on superhelical density of the cleavage indicate that intercalated ethidium is mainly responsible for nicking DNA. Superoxide dismutase has littl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Deniss IS,Morgan AR

    更新日期:1976-02-01 00:00:00