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Predicting and Characterising Protein-Protein Complexes
Predicting and Characterising Protein-Protein Complexes Iain Hervé Moal June 2011 Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute and Department of Biochemistry and Molecular Biology, University College London A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Biochemistry at the University College London. 2 I, Iain Hervé Moal, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Abstract Macromolecular interactions play a key role in all life processes. The con- struction and annotation of protein interaction networks is pivotal for the understanding of these processes, and how their perturbation leads to dis- ease. However the extent of the human interactome and the limitations of the experimental techniques which can be brought to bear upon it necessit- ate theoretical approaches. Presented here are computational investigations into the interactions between biological macromolecules, focusing on the structural prediction of interactions, docking, and their kinetic and thermo- dynamic characterisation via empirical functions. Firstly, the use of normal modes in docking is investigated. Vibrational analysis of proteins are shown to indicate the motions which proteins are intrinsically disposed to under- take, and the use of this information to model flexible deformations upon protein-protein binding is evaluated. Subsequently SwarmDock, a docking algorithm which models flexibility as a linear combination of normal modes, is presented and benchmarked on a wide variety of test cases. This algorithm utilises state of the art energy functions and metaheuristics to navigate the free energy landscape. -
Functional Effects Detailed Research Plan
GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data. -
A Moor Propre: Charles Albert Fechter's Othello
A MOOR PROPRE: CHARLES ALBERT FECHTER'S OTHELLO A Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master of Arts in the Graduate School of The Ohio State University By Matthew Scott Phillips, B.A. * * * * * The Ohio State University •· 1992 Thesis Committee: Approved by Alan Woods Joy Reilly Adviser Department of Theatre swift, light-footed, and strange, with his own dark face in a rage,/ Scorning the time-honoured rules Of the actor's conventional schools,/ Tenderly, thoughtfully, earnestly, FECHTER comes on to the stage. (From "The Three Othellos," Fun 9 Nov. 1861: 76.} Copyright by Matthew Scott Phillips ©1992 J • To My Wife Margaret Freehling Phillips ii ACKNOWLEDGEMENTS I express heartfelt appreciation to the members of my thesis committee: to my adviser, Dr. Alan Woods, whose guidance and insight made possible the completion of this thesis, and Dr. Joy Reilly, for whose unflagging encouragement I will be eternally grateful. I would also like to acknowledge the invaluable services of the British Library, the Jerome Lawrence and Robert E. Lee Theatre Research Institute and its curator, Nena Couch. The support and encouragement given me by my family has been outstanding. I thank my father for raising my spirits when I needed it and my mother, whose selflessness has made the fulfillment of so many of my goals possible, for putting up with me. Finally, I would like to thank my wife, Maggie, for her courage, sacrifice and unwavering faith in me. Without her I would not have come this far, and without her I could go no further. -
Development of Novel Strategies for Template-Based Protein Structure Prediction
Imperial College London Department of Life Sciences PhD Thesis Development of novel strategies for template-based protein structure prediction Stefans Mezulis supervised by Prof. Michael Sternberg Prof. William Knottenbelt September 2016 Abstract The most successful methods for predicting the structure of a protein from its sequence rely on identifying homologous sequences with a known struc- ture and building a model from these structures. A key component of these homology modelling pipelines is a model combination method, responsible for combining homologous structures into a coherent whole. Presented in this thesis is poing2, a model combination method using physics-, knowledge- and template-based constraints to assemble proteins us- ing information from known structures. By combining intrinsic bond length, angle and torsional constraints with long- and short-range information ex- tracted from template structures, poing2 assembles simplified protein models using molecular dynamics algorithms. Compared to the widely-used model combination tool MODELLER, poing2 is able to assemble models of ap- proximately equal quality. When supplied only with poor quality templates or templates that do not cover the majority of the query sequence, poing2 significantly outperforms MODELLER. Additionally presented in this work is PhyreStorm, a tool for quickly and accurately aligning the three-dimensional structure of a query protein with the Protein Data Bank (PDB). The PhyreStorm web server provides comprehensive, current and rapid structural comparisons to the protein data bank, providing researchers with another tool from which a range of biological insights may be drawn. By partitioning the PDB into clusters of similar structures and performing an initial alignment to the representatives of each cluster, PhyreStorm is able to quickly determine which structures should be excluded from the alignment. -
Read Ebook {PDF EPUB} Closure a Story of Everything by Hilary Lawson Closure : a Story of Everything PDF
Read Ebook {PDF EPUB} Closure A Story of Everything by Hilary Lawson Closure : A Story of Everything PDF. For over 2000 years our culture has believed in the possibility of a single true account of the world. Now this age is coming to a close. As a result there is a deep unease. We are lost both as individuals, and as a culture. In the new relativistic, post-modern era, we have no history, no right or moral action, and no body of knowledge. In their place is a plethora of alternative, and sometimes incompatible theories from 'fuzzy logic' to 'consilience' proposing a theory of everything. Closure is a response to this crisis. It is a radically new story about the nature of ourselves and of the world. Closure exposes the central questions of contemporary philosophy: language and meaning, of the individual and identity, of truth and reality, but it is also philosophical in the broader everyday sense that it enables us to make sense of where and who we are. A central principle, the process of closure, is shown to be at the heart of experience and language. As a theory of knowledge it has dramatic consequences for our understanding of the sciences, involving a reinterpretation of what science does and how it is able to do it. It similarly proposes a profound shift in the role of art and religion. But, above all, it reshapes our understanding of ourselves and the organisation of society, our goals and our capacity to achieve them. A superb new account of how order is created out of disorder, Closure is an exhilarating work of conceptual geography. -
Centre for Bioinformatics Imperial College London
Centre for Bioinformatics Imperial College London Inaugural Report January 2003 Centre Director: Prof Michael Sternberg www.imperial.ac.uk/bioinformatics [email protected] Support Service Head: Dr Sarah Butcher www.codon.bioinformatics.ic.ac.uk [email protected] Centre for Bioinformatics - Imperial College London - Inaugural Report - January 2003 1 Contents Summary..................................................................................................................... 3 1. Background and Objectives .................................................................................... 4 1.1 Background ....................................................................................................... 4 1.2 Objectives of the Centre for Bioinformatics ....................................................... 4 1.3 Objectives of the Bioinformatics Support Service.............................................. 5 1.4 Historical Notes ................................................................................................. 5 2. Management ........................................................................................................... 6 3. Biographies of the Team......................................................................................... 7 4. Bioinformatics Research at Imperial ....................................................................... 8 4.1 Affiliates of the Centre ....................................................................................... 8 4.2 Research Grants -
Legal Writing As a Kind of Philosophy'
Legal Writing as a Kind of Philosophy' by Joel I. Cornwell* Perhaps what is inexpressible (what I find mysterious and am not able to express) is the background against which whatever I could express has its meaning. -Ludwig Wittgenstein' Literary theory can be said to come into being when the approach to literary texts is no longer based on non-linguistic, that is to say historical and aesthetic, considerations or, to put it somewhat less crudely, when the object of discussion is no longer the meaning or the value but the modalities of production and of reception of meaning and of value prior to their establishment-the implication being that this establishment is problematic enough to require an autonomous discipline of critical investigation to consider its possibility and its status. -Paul de Man2 I. INTRODUCTION Post-structuralist theories of textual meaning have been integrated into legal education in various ways, notably through the influence of the I The title is a play on Richard Rorty's essay on Derrida,Philosophy as a Kind of Writing: An Essay on Derrida, in RICHARD RORTY, CONSEQUENCES OF PRAGMATISM 90 (1982). Devotees of Rorty's essay will note that I have also mimicked the form of his opening paragraphs ("Here is one way to look at. ."). As deconstructionist critics are well aware, there can be no writing without iteration. See JONATHAN CULLER, ON DECONSTRUCTION 110-34 (1994). * Associate Professor of Law, The John Marshall Law School. An earlier draft of this Article was presented at the 1996 Conference of the Legal Writing Institute. 1. -
Seine Fishing on the Dutch and German Parts of the Dogger Bank, 2013-2019
Wageningen Economic Research The mission of Wageningen University & Research is “To explore the potential P.O. Box 29703 of nature to improve the quality of life”. Under the banner Wageningen University Seine fishing on the Dutch and German 2502 LS Den Haag & Research, Wageningen University and the specialised research institutes of The Netherlands the Wageningen Research Foundation have joined forces in contributing to T +31 (0)70 335 83 30 finding solutions to important questions in the domain of healthy food and living parts of the Dogger Bank, 2013-2019 E [email protected] environment. With its roughly 30 branches, 6,500 employees (5,500 fte) and www.wur.eu/economic-research 12,500 students, Wageningen University & Research is one of the leading Overview of the economic importance and the ecologic impact of the Belgian, British, organisations in its domain. The unique Wageningen approach lies in its integrated Danish, Dutch, French, German and Swedish fleets Report 2020-105 approach to issues and the collaboration between different disciplines. ISBN 978-94-6395-597-3 Katell G. Hamon, Sander Glorius, Arie Klok, Jacqueline Tamis, Ruud Jongbloed Seine fishing on the Dutch and German parts of the Dogger Bank, 2013-2019 Overview of the economic importance and the ecologic impact of the Belgian, British, Danish, Dutch, French, German and Swedish fleets Katell G. Hamon,1 Sander Glorius,2 Arie Klok,1 Jacqueline Tamis,2 Ruud Jongbloed2 1 Wageningen Economic Research 2 Wageningen Marine Research This study was carried out by Wageningen University & Research and subsidised by the Dutch Ministry of Agriculture, Nature and Food Quality within the context of the ‘Natuurinclusieve visserij’ research theme of the Policy Support (project number BO-43-023.02-059) Wageningen University & Research Wageningen, November 2020 REPORT 2020-105 ISBN 978-94-6395-597-3 Hamon, K.G., S. -
“Hammerfest” by Bill Bryson Introduction
Generalitat de Catalunya Departamentd’Ensenyament Escoles Oficial d’Idiomes “Hammerfest” by Bill Bryson Introduction William McGuire "Bill" Bryson , OBE , (born December 8, 1951) is a best-selling American author of humorous books on travel, as well as books on the English language and on science. Born an American, he was a resident of Britain for most of his adult life before returning to the US in 1995. In 2003 Bryson moved back to Britain, living in the old rectory of Wramplingham , Norfolk, and was appointed Chancellor of Durham University . Bill Bryson, the author of the set of columns collected in “Notes from a big country,” is an American who wrote travel books and newspapered in England for 20 years before returning to New Hampshire with his wife and family in 1996. This book consists of many chapters, and in each of them the author dwells upon different aspects of life in America. The chapter “So Sue me” is taken from this book. In this chapter the writer reflects on the issue of crime, and mocks at the amount of ridiculous lawsuits with his typical sense of humour In the early seventies, Bill Bryson backpacked across Europe – in search of enlightment, beer, and women. Twenty years later he decided to retrace his journey. The result is the affectionate and riotously funny book Neither here nor there . One of the chapters taken from this book describes the Northen lights and is called “Hammerfest”. This text is full of epithets and is rich in descriptive nouns, adjectives and verbs. The main aim, apart from enjoying reading, is to understand descriptive texts, learn the vocabulary selected by the teacher, use it in the context, gives detailed descriptions. -
Spatial and Bathymetric Distribution of Deepwater Megabenthic Echinoderms in the Malta 25-Nautical Miles Fisheries Management Zone
http://lib.uliege.be https://matheo.uliege.be Spatial and bathymetric distribution of deepwater megabenthic echinoderms in the Malta 25-nautical miles Fisheries Management Zone Auteur : Leonard, Camille Promoteur(s) : Poulicek, Mathieu; 1573 Faculté : Faculté des Sciences Diplôme : Master en biologie des organismes et écologie, à finalité approfondie Année académique : 2016-2017 URI/URL : http://hdl.handle.net/2268.2/3148 Avertissement à l'attention des usagers : Tous les documents placés en accès ouvert sur le site le site MatheO sont protégés par le droit d'auteur. Conformément aux principes énoncés par la "Budapest Open Access Initiative"(BOAI, 2002), l'utilisateur du site peut lire, télécharger, copier, transmettre, imprimer, chercher ou faire un lien vers le texte intégral de ces documents, les disséquer pour les indexer, s'en servir de données pour un logiciel, ou s'en servir à toute autre fin légale (ou prévue par la réglementation relative au droit d'auteur). Toute utilisation du document à des fins commerciales est strictement interdite. Par ailleurs, l'utilisateur s'engage à respecter les droits moraux de l'auteur, principalement le droit à l'intégrité de l'oeuvre et le droit de paternité et ce dans toute utilisation que l'utilisateur entreprend. Ainsi, à titre d'exemple, lorsqu'il reproduira un document par extrait ou dans son intégralité, l'utilisateur citera de manière complète les sources telles que mentionnées ci-dessus. Toute utilisation non explicitement autorisée ci-avant (telle que par exemple, la modification du document ou son résumé) nécessite l'autorisation préalable et expresse des auteurs ou de leurs ayants droit. -
Bill Bryson's Notes from a Big Country As a Critique of American
“Typically American”: Bill Bryson’s Notes from a Big Country as a critique of American society Diplomarbeit zur Erlangung des akademischen Grades eines Magisters der Philosophie an der Karl-Franzens-Universität Graz vorgelegt von Marin Tomic am Institut für Amerikanistik Begutachter: Hölbling Walter, Univ.-Prof. Mag. Dr.phil. Graz, 2011 Table of Contents 1. Introduction ...................................................................................................................... 1 2. Background ...................................................................................................................... 3 2.1. Bill Bryson and his work .................................................................................... 3 2.2. The relevance of stereotypes .............................................................................. 3 2.3. Bryson’ use of stereotypes ................................................................................. 6 2.4. America as a stereotype ...................................................................................... 7 3. The image of the USA ................................................................................................... 8 3.1. America in German Literature ......................................................................... 12 4. The ‘dumb’ American ................................................................................................. 14 4.1. American ignorance ........................................................................................ -
Michel Chion's Audio-Vision Bravely Sets out to Rectify
In Audio-Vision, the French composer-filmmaker-critic Michel Chion presents a reassessment of the audiovisual media since sound's revolutionary debut in 1927 and sheds light on the mutual influ ences of sound and image in audiovisual perception. Chion expands on the arguments from his influential trilogy on sound in cinema—La Voix au cinema, Le Son au cinema, and La Toile trouee—while providing an overview of the functions and aesthetics of sound in film and television. He considers the effects of evolving audiovisual technologies such as widescreen, multi- track sound, and Dolby stereo on audio-vision, influences of sound on the perception of space and time, and contemporary forms of audio-vision embodied in music videos, video art, and commercial television. His final chapter presents a model for audiovisual analysis of film. Walter Murch, who contributes the foreword, has been hon ored by both the British and American Motion Picture Academies for his sound design and picture editing. He is especially well- known for his work on The Godfather, The Conversation, and Apoc alypse Now. "Michel Chion is the leading French cinema scholar to study the sound track. ... I know of no writer in any language to have published as much in this area, and of such uniformly high quality, a, he." ALAN W|LUAMS RUTGERS UNIVERSITY MICHEL CHION is an experimental composer, a director of short films, and a critic for Cahiers du cinema. He has pub lished books on screenwriting, Jacques Tati, David Lynch, and Charlie Chaplin, in addition to his four books on film sound.