PDB) Format Is a Standard for ®Les Containing Atomic Coordinates
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Molecular Symmetry
Molecular Symmetry Symmetry helps us understand molecular structure, some chemical properties, and characteristics of physical properties (spectroscopy) – used with group theory to predict vibrational spectra for the identification of molecular shape, and as a tool for understanding electronic structure and bonding. Symmetrical : implies the species possesses a number of indistinguishable configurations. 1 Group Theory : mathematical treatment of symmetry. symmetry operation – an operation performed on an object which leaves it in a configuration that is indistinguishable from, and superimposable on, the original configuration. symmetry elements – the points, lines, or planes to which a symmetry operation is carried out. Element Operation Symbol Identity Identity E Symmetry plane Reflection in the plane σ Inversion center Inversion of a point x,y,z to -x,-y,-z i Proper axis Rotation by (360/n)° Cn 1. Rotation by (360/n)° Improper axis S 2. Reflection in plane perpendicular to rotation axis n Proper axes of rotation (C n) Rotation with respect to a line (axis of rotation). •Cn is a rotation of (360/n)°. •C2 = 180° rotation, C 3 = 120° rotation, C 4 = 90° rotation, C 5 = 72° rotation, C 6 = 60° rotation… •Each rotation brings you to an indistinguishable state from the original. However, rotation by 90° about the same axis does not give back the identical molecule. XeF 4 is square planar. Therefore H 2O does NOT possess It has four different C 2 axes. a C 4 symmetry axis. A C 4 axis out of the page is called the principle axis because it has the largest n . By convention, the principle axis is in the z-direction 2 3 Reflection through a planes of symmetry (mirror plane) If reflection of all parts of a molecule through a plane produced an indistinguishable configuration, the symmetry element is called a mirror plane or plane of symmetry . -
Superheroes Trivia Quiz Iv
SUPERHEROES TRIVIA QUIZ IV ( www.TriviaChamp.com ) 1> Which superhero carries an indestructible shield? a. The Green Lantern b. Captain America c. Captain Flag d. The Red Tornado 2> Which character is often romantically paired with Batman? a. The Black Canary b. Miss America c. Catwoman d. Hawkgirl 3> Which superhero started out as a petty criminal? a. The Atom b. Spiderman c. The Blue Knight d. Plastic Man 4> Which superhero's alter ego is Raymond Palmer? a. The Atom b. Hawkman c. The Green Arrow d. The Tornado 5> Which superhero is associated with the phrase, "With great power there must also come great responsibility"? a. Spiderman b. Hell Boy c. Batman d. The Hulk 6> Which superhero is nicknamed the "Scarlett Speedster"? a. The Flash b. Speedball c. Stardust d. The Thing 7> Which superhero is dubbed the "Man without Fear"? a. Daredevil b. The Flash c. Wolverine d. Green Lantern 8> Which superhero is the medical doctor for the X-men? a. Storm b. Shadowcat c. Ice Man d. The Beast 9> Who is Batgirl's father (Barbara Gordon)? a. The Mayor b. The Governor c. Batman's Butler d. The Chief of Police 10> Which superhero gains his power from a ring? a. The Green Lantern b. Storm c. Dazzler d. The Hulk 11> Which superhero can manipulate the weather? a. The Tornado b. The Atom c. Strom d. The Thing 12> Which Island does Wonder Woman call home? a. Emerald Island b. Paradise Island c. Amazonia d. Eden Isle 13> Where does the Green Arrow operate? a. -
Impact of the Protein Data Bank Across Scientific Disciplines.Data Science Journal, 19: 25, Pp
Feng, Z, et al. 2020. Impact of the Protein Data Bank Across Scientific Disciplines. Data Science Journal, 19: 25, pp. 1–14. DOI: https://doi.org/10.5334/dsj-2020-025 RESEARCH PAPER Impact of the Protein Data Bank Across Scientific Disciplines Zukang Feng1,2, Natalie Verdiguel3, Luigi Di Costanzo1,4, David S. Goodsell1,5, John D. Westbrook1,2, Stephen K. Burley1,2,6,7,8 and Christine Zardecki1,2 1 Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, US 2 Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, US 3 University of Central Florida, Orlando, Florida, US 4 Department of Agricultural Sciences, University of Naples Federico II, Portici, IT 5 Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, US 6 Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, US 7 Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, US 8 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, US Corresponding author: Christine Zardecki ([email protected]) The Protein Data Bank archive (PDB) was established in 1971 as the 1st open access digital data resource for biology and medicine. Today, the PDB contains >160,000 atomic-level, experimentally-determined 3D biomolecular structures. PDB data are freely and publicly available for download, without restrictions. Each entry contains summary information about the structure and experiment, atomic coordinates, and in most cases, a citation to a corresponding scien- tific publication. -
Archives - Search
Current Auctions Navigation All Archives - Search Category: ALL Archive: BIDDING CLOSED! Over 150 Silver Age Comic Books by DC, Marvel, Gold Key, Dell, More! North (167 records) Lima, OH - WEDNESDAY, November 25th, 2020 Begins closing at 6:30pm at 2 items per minute Item Description Price ITEM Description 500 1966 DC Batman #183 Aug. "Holy Emergency" 10.00 501 1966 DC Batman #186 Nov. "The Jokers Original Robberies" 13.00 502 1966 DC Batman #188 Dec. "The Ten Best Dressed Corpses in Gotham City" 7.50 503 1966 DC Batman #190 Mar. "The Penguin and his Weapon-Umbrella Army against Batman and Robin" 10.00 504 1967 DC Batman #192 June. "The Crystal Ball that Betrayed Batman" 4.50 505 1967 DC Batman #195 Sept. "The Spark-Spangled See-Through Man" 4.50 506 1967 DC Batman #197 Dec. "Catwoman sets her Claws for Batman" 37.00 507 1967 DC Batman #193 Aug. 80pg Giant G37 "6 Suspense Filled Thrillers" 8.00 508 1967 DC Batman #198 Feb. 80pg Giant G43 "Remember? This is the Moment that Changed My Life!" 8.50 509 1967 Marvel Comics Group Fantastic Four #69 Dec. "By Ben Betrayed!" 6.50 510 1967 Marvel Comics Group Fantastic Four #66 Dec. "What Lurks Behind the Beehive?" 41.50 511 1967 Marvel Comics Group The Mighty Thor #143 Aug. "Balder the Brave!" 6.50 512 1967 Marvel Comics Group The Mighty Thor #144 Sept. "This Battleground Earth!" 5.50 513 1967 Marvel Comics Group The Mighty Thor #146 Nov. "...If the Thunder Be Gone!" 5.50 514 1969 Marvel Comics Group The Mighty Thor #166 July. -
Hawkman in the Bronze Age!
HAWKMAN IN THE BRONZE AGE! July 2017 No.97 ™ $8.95 Hawkman TM & © DC Comics. All Rights Reserved. BIRD PEOPLE ISSUE: Hawkworld! Hawk and Dove! Nightwing! Penguin! Blue Falcon! Condorman! featuring Dixon • Howell • Isabella • Kesel • Liefeld McDaniel • Starlin • Truman & more! 1 82658 00097 4 Volume 1, Number 97 July 2017 EDITOR-IN-CHIEF Michael Eury PUBLISHER John Morrow Comics’ Bronze Age and Beyond! DESIGNER Rich Fowlks COVER ARTIST George Pérez (Commissioned illustration from the collection of Aric Shapiro.) COVER COLORIST Glenn Whitmore COVER DESIGNER Michael Kronenberg PROOFREADER Rob Smentek SPECIAL THANKS Alter Ego Karl Kesel Jim Amash Rob Liefeld Mike Baron Tom Lyle Alan Brennert Andy Mangels Marc Buxton Scott McDaniel John Byrne Dan Mishkin BACK SEAT DRIVER: Editorial by Michael Eury ............................2 Oswald Cobblepot Graham Nolan Greg Crosby Dennis O’Neil FLASHBACK: Hawkman in the Bronze Age ...............................3 DC Comics John Ostrander Joel Davidson George Pérez From guest-shots to a Shadow War, the Winged Wonder’s ’70s and ’80s appearances Teresa R. Davidson Todd Reis Chuck Dixon Bob Rozakis ONE-HIT WONDERS: DC Comics Presents #37: Hawkgirl’s First Solo Flight .......21 Justin Francoeur Brenda Rubin A gander at the Superman/Hawkgirl team-up by Jim Starlin and Roy Thomas (DCinthe80s.com) Bart Sears José Luís García-López Aric Shapiro Hawkman TM & © DC Comics. Joe Giella Steve Skeates PRO2PRO ROUNDTABLE: Exploring Hawkworld ...........................23 Mike Gold Anthony Snyder The post-Crisis version of Hawkman, with Timothy Truman, Mike Gold, John Ostrander, and Grand Comics Jim Starlin Graham Nolan Database Bryan D. Stroud Alan Grant Roy Thomas Robert Greenberger Steven Thompson BRING ON THE BAD GUYS: The Penguin, Gotham’s Gentleman of Crime .......31 Mike Grell Titans Tower Numerous creators survey the history of the Man of a Thousand Umbrellas Greg Guler (titanstower.com) Jack C. -
Pdbefold Tutorial Tutorial Pdbefold Can May Be Accessed from Multiple Locations on the Pdbe Website
PDBe TUTORIAL PDBeFold (SSM: Secondary Structure Matching) http://pdbe.org/fold/ This PDBe tutorial introduces PDBeFold, an interactive service for comparing protein structures in 3D. This service provides: . Pairwise and multiple comparison and 3D alignment of protein structures . Examination of a protein structure for similarity with the whole Protein Data Bank (PDB) archive or SCOP. Best C -alignment of compared structures . Download and visualisation of best-superposed structures using various graphical packages PDBeFold structure alignment is based on identification of residues occupying “equivalent” geometrical positions. In other words, unlike sequence alignment, residue type is neglected. The PDBeFold service is a very powerful structure alignment tool which can perform both pairwise and multiple three dimensional alignment. In addition to this there are various options by which the results of the structural alignment query can be sorted. The results of the Secondary Structure Matching can be sorted based on the Q score (Cα- alignment), P score (taking into account RMSD, number of aligned residues, number of gaps, number of matched Secondary Structure Elements and the SSE match score), Z score (based on Gaussian Statistics), RMSD and % Sequence Identity. It is hoped that at the end of this tutorial users will be able to use PDbeFold for the analysis of their own uploaded structures or entries already in the PDB archive. Protein Data Bank in Europe http://pdbe.org PDBeFOLD Tutorial Tutorial PDBeFold can may be accessed from multiple locations on the PDBe website. From the PDBe home page (http://pdbe.org/), there are two access points for the program as shown below. -
Lab 1. Bond Character and Molecular Polarity: How Does Atom Electronegativity Affect Bond Character and Molecular Polarity?
Lab 1. Bond Character and Molecular Polarity: How Does Atom Electronegativity Affect Bond Character and Molecular Polarity? Introduction Chemists often classify chemical compounds into one of two broad categories. The first category is molecular compounds, and the second category is ionic compounds. Molecular compounds consist of atoms that are held together by covalent bonds. Ionic compounds, in contrast, are composed of positive and negative ions that are joined by ionic bonds. Covalent bonds are formed when atoms share one or more pairs of electrons. An ionic bond is formed when one or more electrons from one atom are transferred to another atom. The transfer of one or more electrons from one atom to another results in the formation of a positive ion and a negative ion. The ions then attract each other because they have opposite electrical charges. The term electronegativity refers to a measure of an atom’s tendency to attract electrons from other atoms. Atom electronegativity affects the nature or the character of the bond that will form between two atoms. The electronegativity of atoms also affects the electrical charge of a molecular compound. In some molecules, the electronegativity of the atoms that make up the molecule results in one side of the molecule having a partial negative electrical charge and the other side having a partial positive charge. When this happens, the molecule is described as being polar. Water is an example of a polar molecule because the oxygen side of the molecule has a partial negative charge and the hydrogen side of the molecule has a partial positive charge. -
EMBL-EBI-Overview.Pdf
EMBL-EBI Overview EMBL-EBI Overview Welcome Welcome to the European Bioinformatics Institute (EMBL-EBI), a global hub for big data in biology. We promote scientific progress by providing freely available data to the life-science research community, and by conducting exceptional research in computational biology. At EMBL-EBI, we manage public life-science data on a very large scale, offering a rich resource of carefully curated information. We make our data, tools and infrastructure openly available to an increasingly data-driven scientific community, adjusting to the changing needs of our users, researchers, trainees and industry partners. This proactive approach allows us to deliver relevant, up-to-date data and tools to the millions of scientists who depend on our services. We are a founding member of ELIXIR, the European infrastructure for biological information, and are central to global efforts to exchange information, set standards, develop new methods and curate complex information. Our core databases are produced in collaboration with other world leaders including the National Center for Biotechnology Information in the US, the National Institute of Genetics in Japan, SIB Swiss Institute of Bioinformatics and the Wellcome Trust Sanger Institute in the UK. We are also a world leader in computational biology research, and are well integrated with experimental and computational groups on all EMBL sites. Our research programme is highly collaborative and interdisciplinary, regularly producing high-impact works on sequence and structural alignment, genome analysis, basic biological breakthroughs, algorithms and methods of widespread importance. EMBL-EBI is an international treaty organisation, and we serve the global scientific community. -
Human Genetics 1990–2009
Portfolio Review Human Genetics 1990–2009 June 2010 Acknowledgements The Wellcome Trust would like to thank the many people who generously gave up their time to participate in this review. The project was led by Liz Allen, Michael Dunn and Claire Vaughan. Key input and support was provided by Dave Carr, Kevin Dolby, Audrey Duncanson, Katherine Littler, Suzi Morris, Annie Sanderson and Jo Scott (landscaping analysis), and Lois Reynolds and Tilli Tansey (Wellcome Trust Expert Group). We also would like to thank David Lynn for his ongoing support to the review. The views expressed in this report are those of the Wellcome Trust project team – drawing on the evidence compiled during the review. We are indebted to the independent Expert Group, who were pivotal in providing the assessments of the Wellcome Trust’s role in supporting human genetics and have informed ‘our’ speculations for the future. Finally, we would like to thank Professor Francis Collins, who provided valuable input to the development of the timelines. The Wellcome Trust is a charity registered in England and Wales, no. 210183. Contents Acknowledgements 2 Overview and key findings 4 Landmarks in human genetics 6 1. Introduction and background 8 2. Human genetics research: the global research landscape 9 2.1 Human genetics publication output: 1989–2008 10 3. Looking back: the Wellcome Trust and human genetics 14 3.1 Building research capacity and infrastructure 14 3.1.1 Wellcome Trust Sanger Institute (WTSI) 15 3.1.2 Wellcome Trust Centre for Human Genetics 15 3.1.3 Collaborations, consortia and partnerships 16 3.1.4 Research resources and data 16 3.2 Advancing knowledge and making discoveries 17 3.3 Advancing knowledge and making discoveries: within the field of human genetics 18 3.4 Advancing knowledge and making discoveries: beyond the field of human genetics – ‘ripple’ effects 19 Case studies 22 4. -
Cold War Fantasies: Testing the Limits of the Familial Body Wonder
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by E-space: Manchester Metropolitan University's Research Repository Cold War Fantasies: Testing the Limits of the Familial Body Wonder Woman 1947-1967 was written by Robert Kanigher - the longest writing stint of any in her seventy year history. Kanigher revamped the character in 1958 to fit a more cosy post-Wertham storyline where she lived a fantasy existence on Paradise Island. The images, drawn mainly by Ross Andru and Mike Esposito softened Wonder Woman's image from a warrior woman to a teen romance heroine with a doe-eyes and full lips. Instead of warrior boots she wore Greek sandals tied up with straps around her legs. Kanigher also introduced more stories of life on Paradise Island and they must have been popular with readers because they featured in sixteen out of the twenty-three issues in this era. Also Wonder Woman appeared in the top thirty best selling comics with a readership of over 200,000.1 The demands by readers for more of these stories in letters pages and within the storylines themselves, demonstrate they must have hailed, some aspects of readers' lives in Cold War America. Yet despite her popularity, this era is one of the most overlooked in Wonder Woman scholarship, possibly because the stories were regarded as fairytales told to a teenage female readership. Yet this era throws up some fascinating cultural paradoxes. Wonder Woman posed a problem in 1950s and '60s because she challenged the perceived role of women as reliant on men in family life and the job market. -
Jlunlimitedchecklist
WWW.HEROCLIXIN.COM WWW.HEROCLIXIN.COM WWW.HEROCLIXIN.COM WWW.HEROCLIXIN.COM 001_____SUPERMAN .......................................................... 100 C 001_____SUPERMAN .......................................................... 100 C TEAM-UP CARDS (1 of 2) TEAM-UP CARDS (2 of 2) 002_____GREEN LANTERN .................................................. 65 C 002_____GREEN LANTERN .................................................. 65 C 003_____THE FLASH ............................................................. 30 C 003_____THE FLASH ............................................................. 30 C SUPERMAN GREEN ARROW 004_____DR. FATE .........................................................65 - 10 C 004_____DR. FATE .........................................................65 - 10 C 001.01 _____TEAM UP: GREEN LANTERN 026.01 _____TEAM UP: SUPERMAN 005a____BATMAN .................................................................. 70 C 005a____BATMAN .................................................................. 70 C 001.02 _____TEAM UP: BATMAN 026.02 _____TEAM UP: GREEN LANTERN 005b____BATMAN .................................................................. 40 P 005b____BATMAN .................................................................. 40 P 001.03 _____TEAM UP: WONDER WOMAN 026.03 _____TEAM UP: BATMAN 006_____CADMUS LABS SCIENTIST ................................... 15 C 006_____CADMUS LABS SCIENTIST ................................... 15 C 001.04 _____TEAM UP: THE FLASH 026.04 _____TEAM UP: WONDER WOMAN 007_____S.T.A.R. -
EC-PSI: Associating Enzyme Commission Numbers with Pfam Domains
bioRxiv preprint doi: https://doi.org/10.1101/022343; this version posted July 10, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. EC-PSI: Associating Enzyme Commission Numbers with Pfam Domains Seyed Ziaeddin ALBORZI1;2, Marie-Dominique DEVIGNES3 and David W. RITCHIE2 1 Universite´ de Lorraine, LORIA, UMR 7503, Vandœuvre-les-Nancy,` F-54506, France 2 INRIA, Villers-les-Nancy,` F-54600, France 3 CNRS, LORIA, UMR 7503, Vandœuvre-les-Nancy,` F-54506, France Corresponding Author: [email protected] Abstract With the growing number of protein structures in the protein data bank (PDB), there is a need to annotate these structures at the domain level in order to relate protein structure to protein function. Thanks to the SIFTS database, many PDB chains are now cross-referenced with Pfam domains and enzyme commission (EC) numbers. However, these annotations do not include any explicit relationship between individual Pfam domains and EC numbers. This article presents a novel statistical training-based method called EC-PSI that can automatically infer high confi- dence associations between EC numbers and Pfam domains directly from EC-chain associations from SIFTS and from EC-sequence associations from the SwissProt, and TrEMBL databases. By collecting and integrating these existing EC-chain/sequence annotations, our approach is able to infer a total of 8,329 direct EC-Pfam associations with an overall F-measure of 0.819 with respect to the manually curated InterPro database, which we treat here as a “gold standard” reference dataset.