当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures.

EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures.

Abstract：

:EzMol is a molecular visualization Web server in the form of a software wizard, located at http://www.sbg.bio.ic.ac.uk/ezmol/. It is designed for easy and rapid image manipulation and display of protein molecules, and is intended for users who need to quickly produce high-resolution images of protein molecules but do not have the time or inclination to use a software molecular visualization system. EzMol allows the upload of molecular structure files in PDB format to generate a Web page including a representation of the structure that the user can manipulate. EzMol provides intuitive options for chain display, adjusting the color/transparency of residues, side chains and protein surfaces, and for adding labels to residues. The final adjusted protein image can then be downloaded as a high-resolution image. There are a range of applications for rapid protein display, including the illustration of specific areas of a protein structure and the rapid prototyping of images.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Reynolds CR,Islam SA,Sternberg MJE

doi

10.1016/j.jmb.2018.01.013

subject

Has Abstract

pub_date

2018-07-20 00:00:00

pages

2244-2248

issue

15

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(18)30039-1

journal_volume

430

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29.

    abstract：:The ATPase activity of the DNA packaging protein gp16 (gene product 16) of bacteriophage phi 29 was studied in the completely defined in-vitro assembly system. ATP was hydrolyzed to ADP and Pi in the packaging reaction that included purified proheads, DNA-gp3 and gp16. Approximately one molecule of ATP was used in the...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90121-5

    authors： Guo P,Peterson C,Anderson D

    更新日期：1987-09-20 00:00:00

  • Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity.

    abstract：:Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.12.010

    authors： Welin M,Wang L,Eriksson S,Eklund H

    更新日期：2007-03-09 00:00:00

  • ATP synthase from bovine heart mitochondria. In vitro assembly of a stalk complex in the presence of F1-ATPase and in its absence.

    abstract：:Four subunits of the F1F0-ATPase from bovine heart mitochondria have been produced by heterologous over-expression in Escherichia coli. They are the oligomycin sensitivity conferral protein (OSCP), coupling factor 6 (F6) and subunits b and d. Likewise, fragments b', bI, bC, and bM (amino acid residues 79 to 214, 121 t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1591

    authors： Collinson IR,van Raaij MJ,Runswick MJ,Fearnley IM,Skehel JM,Orriss GL,Miroux B,Walker JE

    更新日期：1994-09-30 00:00:00

  • The structure of Escherichia coli cytosine deaminase.

    abstract：:Cytosine deaminase (CD) catalyzes the deamination of cytosine, producing uracil. This enzyme is present in prokaryotes and fungi (but not multicellular eukaryotes) and is an important member of the pyrimidine salvage pathway in those organisms. The same enzyme also catalyzes the conversion of 5-fluorocytosine to 5-flu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5277

    authors： Ireton GC,McDermott G,Black ME,Stoddard BL

    更新日期：2002-01-25 00:00:00

  • Reduced misreading of asparagine codons by Escherichia coli tRNALys with hypomodified derivatives of 5-methylaminomethyl-2-thiouridine in the wobble position.

    abstract：:It has been suggested that modified nucleosides of the xm5(s2)U(m)34-type restrict the wobble capacity of the base, and that their function is to prevent misreading in the third position of the codon in mixed codon family boxes that encode two different amino acids. In this study in Escherichia coli, the misreading in...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2162

    authors： Hagervall TG,Pomerantz SC,McCloskey JA

    更新日期：1998-11-20 00:00:00

  • Analysis of the human Alu Ya-lineage.

    abstract：:The Alu Ya-lineage is a group of related, short interspersed elements (SINEs) found in primates. This lineage includes subfamilies Ya1-Ya5, Ya5a2 and others. Some of these subfamilies are still actively mobilizing in the human genome. We have analyzed 2482 elements that reside in the human genome draft sequence and fo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.07.016

    authors： Otieno AC,Carter AB,Hedges DJ,Walker JA,Ray DA,Garber RK,Anders BA,Stoilova N,Laborde ME,Fowlkes JD,Huang CH,Perodeau B,Batzer MA

    更新日期：2004-09-03 00:00:00

  • Fibrillization propensity for short designed hexapeptides predicted by computer simulation.

    abstract：:Assembly of normally soluble proteins into ordered aggregates, known as amyloid fibrils, is a cause or associated symptom of numerous human disorders, including Alzheimer's and the prion diseases. Here, we test the ability of discontinuous molecular dynamics (DMD) simulations based on PRIME20, a new intermediate-resol...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.12.038

    authors： Wagoner VA,Cheon M,Chang I,Hall CK

    更新日期：2012-03-02 00:00:00

  • Engineered Bacillus lentus subtilisins having altered flexibility.

    abstract：:The three-dimensional structures of engineered variants of Bacillus lentus subtilisin having increased enzymatic activity, K27R/N87S/V104Y/N123S/T274A (RSYSA) and N76D/N87S/S103A/V104I (DSAI), were determined by X-ray crystallography. In addition to identifying changes in atomic position we report a method that identi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3033

    authors： Graycar T,Knapp M,Ganshaw G,Dauberman J,Bott R

    更新日期：1999-09-10 00:00:00

  • Topological frustration and the folding of interleukin-1 beta.

    abstract：:The cytokine, interleukin-1beta (IL-1beta), adopts a beta-trefoil fold. It is known to be much slower folding than similarly sized proteins, despite having a low contact order. Proteins are sufficiently well designed that their folding is not dominated by local energetic traps. Therefore, protein models that encode on...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.11.074

    authors： Gosavi S,Chavez LL,Jennings PA,Onuchic JN

    更新日期：2006-03-31 00:00:00

  • Complementary DNA cloning of a protein highly homologous to mammalian sarcoplasmic reticulum Ca-ATPase from the crustacean Artemia.

    abstract：:Complementary DNA clones coding for an Artemia ATPase have been isolated using an oligonucleotide probe for a region highly conserved between P-type ATPases. The nucleotide sequence of three overlapping clones, 3309 base-pairs, has been established. This sequence includes 78 nucleotides of 5' untranslated sequence, an...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90106-x

    authors： Palmero I,Sastre L

    更新日期：1989-12-20 00:00:00

  • Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin.

    abstract：:To study mechanisms of nucleosome positioning, small circular plasmids were constructed, assembled into chromatin in vivo in Saccharomyces cerevisiae, and their chromatin structures were analysed with respect to positions of nucleosomes and nuclease-sensitive regions. Plasmids used include insertions of the URA3 gene ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90291-3

    authors： Thoma F

    更新日期：1986-07-20 00:00:00

  • Autoinhibition of ETV6 (TEL) DNA binding: appended helices sterically block the ETS domain.

    abstract：:ETV6 (or TEL), a transcriptional repressor belonging to the ETS family, is frequently involved in chromosomal translocations linked with human cancers. It displays a DNA-binding mode distinct from other ETS proteins due to the presence of a self-associating PNT domain. In this study, we used NMR spectroscopy to dissec...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.05.010

    authors： Coyne HJ 3rd,De S,Okon M,Green SM,Bhachech N,Graves BJ,McIntosh LP

    更新日期：2012-08-03 00:00:00

  • Cooperation of TOM and TIM23 complexes during translocation of proteins into mitochondria.

    abstract：:Translocation of the majority of mitochondrial proteins from the cytosol into mitochondria requires the cooperation of TOM and TIM23 complexes in the outer and inner mitochondrial membranes. The molecular mechanisms underlying this cooperation remain largely unknown. Here, we present biochemical and genetic evidence t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.07.015

    authors： Waegemann K,Popov-Čeleketić D,Neupert W,Azem A,Mokranjac D

    更新日期：2015-03-13 00:00:00

  • Crystal structure of ferric Aplysia limacina myoglobin at 2 X 0 A resolution.

    abstract：:The three-dimensional structure of ferric myoglobin from the mollusc Aplysia limacina has been refined at 2 X 0 A resolution. The crystallographic R factor, calculated at this stage, is 0 X 194. Despite its high content of apolar residues (both aromatic and aliphatic), Aplysia limacina myoglobin, which contains only o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90285-2

    authors： Bolognesi M,Coda A,Gatti G,Ascenzi P,Brunori M

    更新日期：1985-05-05 00:00:00

  • Transcriptional regulation of mouse alphaB- and gammaF-crystallin genes in lens: opposite promoter-specific interactions between Pax6 and large Maf transcription factors.

    abstract：:Mammalian alphaB-crystallin is highly expressed both in lens epithelium and lens fibers. In contrast, gammaF-crystallin is highly expressed in the lens fiber cells. Crystallin gene expression in lens is regulated at the level of transcription by a sparse number of specific DNA-binding transcription factors. Here, we r...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.07.102

    authors： Yang Y,Chauhan BK,Cveklova K,Cvekl A

    更新日期：2004-11-19 00:00:00

  • Location of high and low affinity fatty acid binding sites on human serum albumin revealed by NMR drug-competition analysis.

    abstract：:Human serum albumin (HSA) is an abundant plasma protein that transports a wide variety of drugs and endogenous compounds. The complex binding capacity of HSA has made it a challenging system to study in detail but in order to develop our understanding of the interactions between ligands for HSA, the locations and rela...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.06.028

    authors： Simard JR,Zunszain PA,Hamilton JA,Curry S

    更新日期：2006-08-11 00:00:00

  • Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.

    abstract：:RNA helicases play fundamental roles in modulating RNA structures and facilitating RNA-protein (RNP) complex assembly in vivo. Previously, our laboratory demonstrated that the DEAD-box RNA helicase Dbp2 in Saccharomyces cerevisiae is required to promote efficient assembly of the co-transcriptionally associated mRNA-bi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.02.005

    authors： Ma WK,Paudel BP,Xing Z,Sabath IG,Rueda D,Tran EJ

    更新日期：2016-03-27 00:00:00

  • Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer.

    abstract：:Many proteins are composed of independently-folded domains connected by flexible linkers. The primary sequence and length of such linkers can set the effective concentration for the tethered domains, which impacts rates of association and enzyme activity. The length of such linkers can be sensitive to environmental co...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.166793

    authors： Basak S,Sakia N,Dougherty L,Guo Z,Wu F,Mindlin F,Lary JW,Cole JL,Ding F,Bowen ME

    更新日期：2021-01-01 00:00:00

  • IS1-mediated tandem duplication of plasmid pBR322. Dependence on recA and on DNA polymerase I.

    abstract：:Transposable-element-mediated fusion of the conjugal plasmid pOX38::Tn9 with pBR322 results in the appearance of cointegrates composed of a single copy of each plasmid, and cointegrates which carry a single copy of pOX38 but multiple tandem copies of pBR322. These plasmids are separated by directly repeated copies of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(83)80249-6

    authors： Chandler M,Galas DJ

    更新日期：1983-03-25 00:00:00

  • Structure, evolutionary conservation, and conformational dynamics of Homo sapiens fascin-1, an F-actin crosslinking protein.

    abstract：:Eukaryotes have several highly conserved actin-binding proteins that crosslink filamentous actin into compact ordered bundles present in distinct cytoskeletal processes, including microvilli, stereocilia and filopodia. Fascin is an actin-binding protein that is present predominantly in filopodia, which are believed to...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.04.043

    authors： Sedeh RS,Fedorov AA,Fedorov EV,Ono S,Matsumura F,Almo SC,Bathe M

    更新日期：2010-07-16 00:00:00

  • Parallel and antiparallel Holliday junctions differ in structure and stability.

    abstract：:Two Holliday junction analogs, JA and JP, containing identical base-paired arms have been constructed from oligonucleotides. The former is constrained to adopt an antiparallel Sigal-Alberts structure, and the latter a parallel structure, by means of single strand d(T)9 tethers. We evaluate here the free energy differe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90942-y

    authors： Lu M,Guo Q,Seeman NC,Kallenbach NR

    更新日期：1991-10-20 00:00:00

  • Primate evolution of the alpha-globin gene cluster and its Alu-like repeats.

    abstract：:The arrangement of alpha-globin genes in Old World and New World monkeys and a prosimian, galago, has been determined by restriction mapping. Recombinant DNAs containing galago and Old World monkey alpha-globin genes have been isolated and subjected to a partial sequence determination for comparison to alpha-globin ge...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90022-7

    authors： Sawada I,Schmid CW

    更新日期：1986-12-20 00:00:00

  • Infrared dichroism of twisted beta-sheet barrels. The structure of E. coli outer membrane proteins.

    abstract：:The infrared dichroic ratios of the amide bands from oriented beta-barrels yield an experimental value for the mean orientation, beta, of the beta-strands, relative to the barrel axis. For a barrel of n strands, this then gives the shear number, S, that characterizes the stagger of the beta-sheet. Combining values of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3557

    authors： Marsh D

    更新日期：2000-03-31 00:00:00

  • Interaction of crystalline tyrosyl-tRNA synthetase with adenosine, adenosine monophosphate, adenosine triphosphate and pyrophosphate in the presence of tyrosinol.

    abstract：:Crystalline complexes of tyrosyl-tRNA synthetase from Bacillus stearothermophilus were prepared with adenosine, AMP, ATP and PPi, all in the presence of tyrosinol, which binds strongly to the tyrosine binding site but cannot be adenylated by ATP. The hydrolysis of ATP in the presence of crystalline tyrosyl-tRNA synthe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(84)90392-9

    authors： Monteilhet C,Blow DM,Brick P

    更新日期：1984-03-15 00:00:00

  • Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome.

    abstract：:The Escherichia coli RNA degradosome is a multienzyme assembly that functions in transcript turnover and maturation of structured RNA precursors. We have developed a procedure to reconstitute the RNA degradosome from recombinant components using modular coexpression vectors. The reconstituted assembly can be purified ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.07.059

    authors： Worrall JA,Górna M,Crump NT,Phillips LG,Tuck AC,Price AJ,Bavro VN,Luisi BF

    更新日期：2008-10-17 00:00:00

  • Crystallization and X-ray analysis of a multienzyme complex containing RUBISCO and RuBP.

    abstract：:Single crystals of a multienzyme complex isolated from spinach leaves, and containing RUBISCO bound to the substrate RuBP have been grown and characterized. The crystals belong to the orthorhombic space group P2(1)2(1)2 with a = 173 A, b = 134 A and c = 112 A, and contain two enzyme complex molecules in the unit cell....

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1681

    authors： Hosur MV,Sainis JK,Kannan KK

    更新日期：1993-12-20 00:00:00

  • Cooperativity in the thermosome.

    abstract：:The thermosome from Thermoplasma acidophilum is a type II chaperonin composed of eight alpha and eight beta subunits. The genes encoding the two types of subunit were co-expressed in Escherichia coli and the alpha8/beta8 complex purified from the cell extract. The isolated complex showed steady-state ATPase properties...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.01.066

    authors： Bigotti MG,Clarke AR

    更新日期：2005-04-22 00:00:00

  • Predictive QM/MM Modeling of Modulations in Protein-Protein Binding by Lysine Methylation.

    abstract：:Lysine methylation is a key regulator of protein-protein binding. The amine group of lysine can accept up to three methyl groups, and experiments show that protein-protein binding free energies are sensitive to the extent of methylation. These sensitivities have been rationalized in terms of chemical and structural fe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.166745

    authors： Rahman S,Wineman-Fisher V,Al-Hamdani Y,Tkatchenko A,Varma S

    更新日期：2021-02-05 00:00:00

  • The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity.

    abstract：:The structure of a class II fructose-1,6-bisphosphate aldolase in complex with the substrate analogue and inhibitor phosphoglycolohydroxamate (PGH) has been determined using X-ray diffraction terms to a resolution of 2.0 A (1 A=0.1 nm). The crystals are trigonal, space group P3121 with a=b=78.24 A, c=289.69 A. The asy...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2609

    authors： Hall DR,Leonard GA,Reed CD,Watt CI,Berry A,Hunter WN

    更新日期：1999-03-26 00:00:00

  • Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease.

    abstract：:No drug has been targeted specifically for HIV-2 (human immunodeficiency virus type 2) infection despite its increasing prevalence worldwide. The antiviral HIV-1 (human immunodeficiency virus type 1) protease (PR) inhibitor darunavir and the chemically related GRL98065 and GRL06579A were designed with the same chemica...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.09.031

    authors： Kovalevsky AY,Louis JM,Aniana A,Ghosh AK,Weber IT

    更新日期：2008-12-05 00:00:00