Nobel Molecules Number 2 Summer 2007
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21St American Conference on Crystal Growth and Epitaxy (ACCGE-21)
Program Book 21st American Conference on Crystal Growth and Epitaxy (ACCGE-21) and 18th US Workshop on Organometallic Vapor Phase Epitaxy (OMVPE-18) and 3rd Symposium on 2D Electronic Materials and Symposium on Epitaxy of Complex Oxides July 30 – August 4 1 | P a g e Table of Contents Table of Contents ........................................................................................................... 2 Welcome to Santa Fe, New Mexico………………………………...………………………..3 Maps of Conference Area and Resort ............................................................................ 4 Conference Sponsors & Supporters ............................................................................... 7 Conference Exhibitors .................................................................................................... 7 Conference Organizers .................................................................................................. 8 OMVPE Workshop Committee………………………. ...................................................... 9 AACG Organization (2015-2017) ................................................................................. 10 ACCGE Symposia and Organizers .................................................... ………………….11 Plenary Speakers ............................................................................... ………………….13 Award Recipients ............................................................................... ………………….14 Scope and Purpose of the Conferences ...................................................................... -
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. -
Molecular Beam Epitaxial Growth, Characterization, and Nanophotonic Device Applications of Inn Nanowires on Si Platform
Molecular Beam Epitaxial Growth, Characterization, and Nanophotonic Device Applications of InN Nanowires on Si Platform Songrui Zhao Department of Electrical and Computer Engineering Faculty of Engineering McGill University, Montreal April 2013 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Doctor of Philosophy © Songrui Zhao 2013 To my wife, Rubing Table of Contents Acknowledgement ................................................................................................ vi Contribution of Authors .................................................................................... viii List of Figures ....................................................................................................... ix List of Acronyms ................................................................................................ xiii Abstract ............................................................................................................... xiv Abrégé .................................................................................................................. xv 1. Introduction ................................................................................................... 1-1 1.1. The importance of InN to the III-nitride family .................................... 1-2 1.1.1. The importance of InN to In(Ga)N-based devices: An example….. ............................................................................................ 1-3 1.2. Challenges in InN planar structures -
NEWSLETTER Number 2 Summer 2005
AMERICAN CRYSTALLOGRAPHIC ASSOCIATION NEWSLETTER Number 2 Summer 2005 Blood 2,000,000X Art in Crystallography Table of Contents - President's Column Summer 2005 President's Column Table of Contents Presidentʼs Column ..........................................................1-2 I would like to thank all of the volunteers Guest Editorial .................................................................... 2 who do so much for News from Canada .............................................................. 3 the ACA, especially ACA Awards - Warren - Buerger - Etter ...........................6-7 those involved in our Other Awards to ACA Members .......................................7-9 annual meetings. We NAS News - Bridging the Sciences ...............................8-10 had a very successful News from Latin America ............................................10-12 meeting in Orlando, Contributors to this Issue ................................................... 10 FL thanks in large part US National Committee for Crystallography .................... 13 to our Program Chair, Crystmol 2.1 ...................................................................... 14 Edward Collins, Local Chairs, Khalil Abboud 35th Mid-Atlantic Protein Meeting ................................... 15 and Thomas Selby and 16 17th West Coast Protein Workshop ................................... their hard working com- Second Annual SERT-CAT Symposium ........................... 17 mittees. All of our initial GM/CA CAT Dedication .................................................. -
Happy Anniversary, PDB!
FOCUS | EDITORIAL FOCUS | editorial Happy anniversary, PDB! We celebrate the 50th anniversary of the Protein Data Bank together with our colleagues at Nature Methods with a special collection that showcases key achievements in structural biology and views of its future. n October 1971, the establishment of the PDB was also instrumental in the Structural biologists have traditionally of a central open repository for development of software tools that allow the used a ‘divide-and-conquer’ approach to Imacromolecular structure data, the visualization, validation, analysis and storage address these complex questions, analyzing Protein Data Bank (PDB), was announced of protein structure data. In the early days, single proteins or protein domains. This in Nature New Biology (Nat. New Biol. 233, facilitating data access was far from trivial. tactic has in part been necessary due to 223 (1971)). This new repository, which at The process that was created to allow remote technical limitations, but reconstituting the time contained seven structures, was computers to connect and to search data a biological system from its individual the culmination of grassroots efforts led by stored at Brookhaven National Laboratory components in vitro is also an important a cadre of protein crystallographers who was a forerunner to the internet-based pathway toward new knowledge. As Richard were keenly aware of the value of archiving systems that we do not think twice about Feynman aptly put it, “What I cannot create, and sharing X-ray crystallography data, today. As a testament to its success, the I do not understand.” including atomic coordinates, structure PDB now hosts more than 175,000 Despite the success of such reductionist factors and electron density maps. -
Message from the RCSB PDB MESSAGE from the RCSB PDB
Number 23 Fall 2004 Published quart e rly by the Re s e a rch Collabora t o r y for St ru c t u ral Bi o i n f o rmatics Protein Data Ba n k Weekly RCSB PDB news is available on the Web at www.rcsb.org/pdb/latest_news.html Links to RCSB PDB newsletters are available at www.rcsb.org/pdb/newsletter.html C o n t e n t s Message from the RCSB PDB MESSAGE FROM THE RCSB PDB.........................................1 The RCSB PDB attended a variety of meetings this past quarter to demonstrate the use of RCSB tools (such as pdb_extract for structure DATA DEPOSITION AND PROCESSING deposition) and the reengineered RCSB PDB site and database (which 5 Steps for Crystal Structure Deposition .........................2 is still undergoing beta testing at pdbbeta.rcsb.org). PDB Focus: How are HPUB Structures Released?..........2 PDB Deposition Statistics................................................2 Special events at these meetings were also organized by the RCSB: DATA QUERY, REPORTING, AND ACCESS • Together with CCP4, a session aimed at depositors entitled "A RCSB PDB Beta Site .......................................................2 Protein Crystallographic Toolbox: CCP4 Software Suite and RCSB RCSB PDB Presentations & Demonstrations at 3D PDB Deposition Tools" was held at the American Crystallographic SIG/ISMB/ECCB & the Protein Society Meeting...........2 Association's Annual Meeting (ACA; July 17-22; Chicago, IL). Website Statistics .............................................................2 Presentations including "An Introduction to the CCP4 Software Suite", "pdb_extract and CCP4: Making Deposition Easier", and OUTREACH AND EDUCATION "Validation and Deposition at the RCSB Protein Data Bank" can be RCSB PDB Poster Prize Awards.......................................3 downloaded from CCP4 (www.ccp4.ac.uk). -
Doctoral Dissertation
UC San Diego UC San Diego Electronic Theses and Dissertations Title Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis Permalink https://escholarship.org/uc/item/0t54p4gj Author Bliven, Spencer Edward Publication Date 2015 Supplemental Material https://escholarship.org/uc/item/0t54p4gj#supplemental Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Spencer Edward Bliven Committee in charge: Professor Philip E. Bourne, Chair Professor Milton H. Saier, Co-Chair Professor Russell F. Doolittle Professor Michael K. Gilson Professor Adam Godzik 2015 Copyright Spencer Edward Bliven, 2015 All rights reserved. The dissertation of Spencer Edward Bliven is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2015 iii DEDICATION To my father, whose curiosity and enthusiasm for both nature and technology I wholeheartedly share. iv TABLE OF CONTENTS Signature Page................................... iii Dedication...................................... iv Table of Contents..................................v List of Figures.................................... ix List of Tables................................... -
Autodock Vina 1.2.0: New Docking Methods, Expanded Force Field, And
AutoDock Vina 1.2.0: new docking methods, expanded force field, and Python bindings Jerome Eberhardt1,a, , Diogo Santos-Martins1,a, Andreas F. Tillacka, and Stefano Forlia, 1These authors contributed equally to this work. a Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA AutoDock Vina is arguably one of the fastest and most widely plement additional functionality without significant changes used open-source docking engines. However, compared to other in the source code. docking engines in the AutoDock Suite, it lacks features that The usefulness of such specialized methods is hindered by support modeling of specific systems such as macrocycles or the poor search efficiency of AD4. In fact, AD4 can be up modeling water explicitly. Here, we describe the implemen- to 100x slower than Vina 1, depending on the search com- tation of these functionality in AutoDock Vina 1.2.0. Addi- plexity. The large performance difference is due to the bet- tionally, AutoDock Vina 1.2.0 supports the AutoDock4.2 scor- ter search algorithm used in Vina, a Monte-Carlo (MC) iter- ing function, simultaneous docking of multiple ligands, and a 17 batch mode for docking a large number of ligands. Further- ated search combined with the BFGS gradient-based op- more, we implemented Python bindings to facilitate scripting timizer. In comparison with the Lamarckian Genetic Algo- 3 and the development of docking workflows. This work is an ef- rithm (LGA) and Solis-Wets local search of AD4 , the search fort toward the unification of the features of the AutoDock4 and efficiency of Vina leads to better docking results with fewer AutoDock Vina docking engines. -
Hydration Water Dynamics of the Tau Protein in Its Native and Amyloid States Yann Fichou
Hydration water dynamics of the tau protein in its native and amyloid states Yann Fichou To cite this version: Yann Fichou. Hydration water dynamics of the tau protein in its native and amyloid states. Modeling and Simulation. Université Grenoble Alpes, 2015. English. NNT : 2015GREAY021. tel-01214578 HAL Id: tel-01214578 https://tel.archives-ouvertes.fr/tel-01214578 Submitted on 12 Oct 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour obtenir le grade de DOCTEUR DE L’UNIVERSITÉ DE GRENOBLE Spécialité : Physique pour les sciences du vivant Arrêté ministériel : 7 Aout 2006 Présentée par Yann FICHOU Thèse dirigée par Martin WEIK préparée au sein de l’Institut de Biologie Structurale et de l’école doctorale de physique Dynamique de l’eau d’hydratation de la protéine tau dans ses formes native et amyloïde Thèse soutenue publiquement le 11 mars 2015, devant le jury composé de : Pr Antonio Cupane Université de Palerme, Palerme, Italie, Rapporteur Pr Damien Laage Ecole normale supérieure, Paris, France, Rapporteur Dr Martin Blackledge Institut -
Semiconductor Nanowires: Characterization and Surface Modification
Semiconductor Nanowires: Characterization and surface modification Yngman, Sofie 2019 Document Version: Publisher's PDF, also known as Version of record Link to publication Citation for published version (APA): Yngman, S. (2019). Semiconductor Nanowires: Characterization and surface modification. Lund University (Media-Tryck). Total number of authors: 1 General rights Unless other specific re-use rights are stated the following general rights apply: Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Read more about Creative commons licenses: https://creativecommons.org/licenses/ Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. LUND UNIVERSITY PO Box 117 221 00 Lund +46 46-222 00 00 Semiconductor Nanowires Characterization and surface modification SOFIE YNGMAN SYNCHROTRON RADIATION RESEARCH | FACULTY OF SCIENCE | LUND UNIVERSITY Even mobile phone cameras can take pictures of nanowires! Lund University Faculty of Science 952854 Department of Physics Division of Synchrotron Radiation Research 789178 ISBN 978-91-7895-285-4 9 Semiconductor Nanowires: Characterization and surface modification Sofie Yngman DOCTORAL THESIS by due permission of the Faculty of Science, Lund University, Sweden. -
CATALOG Hands On, Minds On! NEW Dynamic DNA Kit©
...where molecules become real TM CATALOG Hands On, Minds On! NEW Dynamic DNA Kit© NOW look at what you can do with our DNA! Page 11 Our Customers’ Favorite Products Tour of a Human Cell I This illustration simulates what we would see if we could K magnify a portion of a living cell by 1,500,000 times. At this H G magnication, atoms would be B about the size of a grain of salt, H cells would be the size of huge buildings, and you would be roughly one-fourth the size of the earth in height, allowing you to J H walk across the continent in a few steps. All of the macromolecules in the cell are shown, including A proteins, nucleic acids, carbohy- B A I drates and lipid bilayers, but all of the smaller molecules have been A D omitted for clarity. In reality, the empty spaces in this picture are lled with water, ions, sugars, ATP, and many other small molecules. A D The narrow strip is taken from a plasma cell (shown above), a cell from the blood that is dedicated to the production of antibodies. The entire process of antibody production is shown, starting from I G the gene in the nucleus, proceeding to synthesis in the endoplasmic reticulum, continuing to processing in the Golgi, and nishing with transport and secretion at the cell surface. C J C C B C D G E G B The Machinery of Life E F F This image is taken from The Machinery of Life by David S. -
RCSB Protein Data Bank Tools for 3D Structure-Guided Cancer Research: Human Papillomavirus (HPV) Case Study
Oncogene (2020) 39:6623–6632 https://doi.org/10.1038/s41388-020-01461-2 REVIEW ARTICLE RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study 1,2 1,3,4,5 David S. Goodsell ● Stephen K. Burley Received: 5 July 2020 / Revised: 30 July 2020 / Accepted: 4 September 2020 / Published online: 16 September 2020 © The Author(s) 2020. This article is published with open access Abstract Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, proliferation, and metastasis. They are also used extensively to identify potentially druggable targets and facilitate discovery and development of both small-molecule and biologic drugs that are today benefiting individuals diagnosed with cancer around the world. 3D structures of biomolecules (including proteins, DNA, RNA, and their complexes with one another, drugs, and other small molecules) are freely distributed by the open-access Protein Data Bank (PDB). This global data repository is used by millions of scientists and educators working in the areas of drug discovery, 1234567890();,: 1234567890();,: vaccine design, and biomedical and biotechnology research. The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers worldwide. Herein, we review online resources made available free of charge by the RCSB PDB to basic and applied researchers, healthcare providers, educators and their students, patients and their families, and the curious public.