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MODELLER 10.1 Manual
MODELLER A Program for Protein Structure Modeling Release 10.1, r12156 Andrej Saliˇ with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-care AT salilab.org URL https://salilab.org/modeller/ 2021/03/12 ii Contents Copyright notice xxi Acknowledgments xxv 1 Introduction 1 1.1 What is Modeller?............................................. 1 1.2 Modeller bibliography....................................... .... 2 1.3 Obtainingandinstallingtheprogram. .................... 3 1.4 Bugreports...................................... ............ 4 1.5 Method for comparative protein structure modeling by Modeller ................... 5 1.6 Using Modeller forcomparativemodeling. ... 8 1.6.1 Preparinginputfiles . ............. 8 1.6.2 Running Modeller ......................................... 9 2 Automated comparative modeling with AutoModel 11 2.1 Simpleusage ..................................... ............ 11 2.2 Moreadvancedusage............................... .............. 12 2.2.1 Including water molecules, HETATM residues, and hydrogenatoms .............. 12 2.2.2 Changing the default optimization and refinement protocol ................... 14 2.2.3 Getting a very fast and approximate model . ................. 14 2.2.4 Building a model from multiple templates . .................. 15 2.2.5 Buildinganallhydrogenmodel -
MODELLER 10.0 Manual
MODELLER A Program for Protein Structure Modeling Release 10.0, r12005 Andrej Saliˇ with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-care AT salilab.org URL https://salilab.org/modeller/ 2021/01/25 ii Contents Copyright notice xxi Acknowledgments xxv 1 Introduction 1 1.1 What is Modeller?............................................. 1 1.2 Modeller bibliography....................................... .... 2 1.3 Obtainingandinstallingtheprogram. .................... 3 1.4 Bugreports...................................... ............ 4 1.5 Method for comparative protein structure modeling by Modeller ................... 5 1.6 Using Modeller forcomparativemodeling. ... 8 1.6.1 Preparinginputfiles . ............. 8 1.6.2 Running Modeller ......................................... 9 2 Automated comparative modeling with AutoModel 11 2.1 Simpleusage ..................................... ............ 11 2.2 Moreadvancedusage............................... .............. 12 2.2.1 Including water molecules, HETATM residues, and hydrogenatoms .............. 12 2.2.2 Changing the default optimization and refinement protocol ................... 14 2.2.3 Getting a very fast and approximate model . ................. 14 2.2.4 Building a model from multiple templates . .................. 15 2.2.5 Buildinganallhydrogenmodel -
Schedule for FDP on Free Open Source Tools for Education and Research Timing Activity About the Activity Webpage Link Opening Talk by Prof
Schedule for FDP on Free Open Source Tools For Education and Research Timing Activity About the activity Webpage Link Opening talk by Prof. D. K. Singh (Director BIT Sindri), 10:00AM - 10:30 AM Inaguration Introdcution of Expert speaker by Coordinator A Spoken Tutorial is a screencast with running 10:30 AM - 11:00 AM Overview of Spoken Tutorials commentary, a recording of computer session created for https://spoken-tutorial.org/ self learning. FOSSEE (Free/Libre and Open Source Software for Education) project promotes the use of FLOSS tools to improve the quality of education in our country. We aim to reduce dependency on proprietary software in 11:00 PM - 11:30 AM Overview of FOSSEE educational institutions. https://fossee.in/ The FOSSEE project is part of the National Mission on Education through Information and Communication Technology (ICT), Ministry of Human Resource Development (MHRD), Government of India. Scilab software, free/libre and open source reference in numerical computation software. Scilab is used in all 11:30 AM - 12:00 PM Scilab and related activities major strategic scientific areas of industry and services https://scilab.in/ such as space, aeronautics, automotive, energy, defense, finance and transport. OpenModelica is a free/libre and open-source environment based on the Modelica modeling language 12:00 PM - 12:30 PM OpenModelica and related activities https://om.fossee.in/ for modeling, simulating, optimizing, and analyzing complex dynamic systems. LUNCH BREAK DWSIM is a multiplatform, CAPE-OPEN compliant chemical process simulator for Windows, Linux, Android, 2:00 PM - 2:30 PM DWSIM and related activities macOS, and iOS. -
Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 11 June 2019 doi:10.20944/preprints201906.0091.v1 Peer-reviewed version available at Biomolecules 2019, 9; doi:10.3390/biom9040123 Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood Abheepsa Mishra1, 2,* and Satyahari Dey1 1Plant Biotechnology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India; [email protected] (A.M.); [email protected] (S.D.) 2Department of Internal Medicine, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA *Correspondence: [email protected]; Tel.:+1(518) 881-9196 Abstract Natural products from plants such as, chemopreventive agents attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide based therapeutics have been developed to combat several health disorders including cancers, metabolic disorders, heart-related, and infectious diseases. Despite the discovery of hundreds of such therapeutic peptides however, only few peptide-based drugs have made it to the market. Moreover, until date the activities of cyclic peptides towards molecular targets such as protein kinases, proteases, and apoptosis related proteins have never been explored. In this study we explore the in silico kinase and protease inhibitor potentials of cyclosaplin as well as study the interactions of cyclosaplin with other cancer-related proteins. -
New Computational Approaches for Investigating the Impact of Mutations on the Transglucosylation Activity of Sucrose Phosphorylase Enzyme
Thesis submitted to the Université de la Réunion for award of Doctor of Philosophy in Sciences speciality in bioinformatics New computational approaches for investigating the impact of mutations on the transglucosylation activity of sucrose phosphorylase enzyme Mahesh VELUSAMY Thesis to be presented on 18th December 2018 in front of the jury composed of Mme Isabelle ANDRE, Directeur de Recherche CNRS, INSA de TOULOUSE, Rapporteur M. Manuel DAUCHEZ, Professeur, Université de Reims Champagne Ardennes, Rapporteur M. Richard DANIELLOU, Professeur, Université d'Orléans, Examinateur M. Yves-Henri SANEJOUAND, Directeur de Recherche CNRS, Université de Nantes, Examinateur Mme Irène MAFFUCCI, Maître de Conférences, Université de Technologie de Compiègne, Examinateur Mme Corinne MIRAL, Maître de Conférences HDR, Université de Nantes, Examinateur M. Frédéric CADET, Professeur, Université de La Réunion, Co-directeur de thèse M. Bernard OFFMANN, Professeur, Université de Nantes, Directeur de thèse ெ்்ந்ி ிைு்ூுத் ெ்யாம் ெ்த உதி்ு ையகு் ானகு் ஆ்ற் அிு. -ிு்ு் ுதி் அ்ப் ுுக், எனு த்ைத ேுாி, தா் க்ூி, அ்ண் ு்ு்ுமா், த்ைக பா்பா, ஆ்தா ுு்மா், ீனா, அ்ண் ்ுக், ெபிய்பா, ெபிய்மா ம்ு் உுுைணயா் இு்த அைண்ு ந்ப்கு்ு் எனு மனமா்்த ந்ி. இ்த ஆ்ி்ைக ுுைம அை3த்ு ுுுத்்காரண், எனு ஆ்ி்ைக இய்ுன் ேபராிிய் ெப்னா்் ஆஃ்ேம். ப்ேு துண்கி் நா் மனதாு், ெபாுளாதார அளிு் க்3்ி் இு்தேபாு, என்ு இ்ெனாு த்ைதயாகே இு்ு எ்ைன பா்்ு்ெகா்3ா். ுி்பாக, எனு ூ்றா் ஆ்ு இுிி், அ்்ு எ்ளோ தி்ப்3 க3ைமக் ம்ு் ிர்ிைனக் இு்தாு், அைத்ெபாு்பு்தாு, அ் என்ு ெ்த ெபாுளாதார உதி, ப்கைB்கழக பிு ம்ு் இதர ி்ாக ்ப்த்ப்3 உதிகு்ு எ்ன ைகமா்ு ெகாு்தாு் ஈ3ாகாு. -
University of Huddersfield Repository
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Huddersfield Repository University of Huddersfield Repository Liang, Shuo, Holmes, Violeta and Kureshi, Ibad Hybrid Computer Cluster with High Flexibility Original Citation Liang, Shuo, Holmes, Violeta and Kureshi, Ibad (2012) Hybrid Computer Cluster with High Flexibility. In: IEEE Cluster 2012, 24-28 September 2012, Beijing, China. This version is available at http://eprints.hud.ac.uk/15840/ The University Repository is a digital collection of the research output of the University, available on Open Access. Copyright and Moral Rights for the items on this site are retained by the individual author and/or other copyright owners. Users may access full items free of charge; copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational or not-for-profit purposes without prior permission or charge, provided: • The authors, title and full bibliographic details is credited in any copy; • A hyperlink and/or URL is included for the original metadata page; and • The content is not changed in any way. For more information, including our policy and submission procedure, please contact the Repository Team at: [email protected]. http://eprints.hud.ac.uk/ Hybrid Computer Cluster with High Flexibility Shuo Liang Dr Violeta Holmes Ibad Kureshi School of Computing and Engineering School of Computing and Engineering School of Computing and Engineering University of Huddersfield University of Huddersfield University of Huddersfield Huddersfield, United Kingdom Huddersfield, United Kingdom Huddersfield, United Kingdom Email: [email protected] Email: [email protected] Email: [email protected] Abstract—In this paper we present a cluster middleware, the others support multi-platform, supplying different user designed to implement a Linux-Windows Hybrid HPC Cluster, interfaces and document support. -
Graduate Brochure 2014 Draft.Pub
THETHE UNIVERSITYUNIVERSITY OFOF MISSOURIMISSOURI——ST.ST. LOUISLOUIS 315 Benton Hall (MC 27) One University Blvd. St. Louis, MO 63121-4400 http://www.umsl.edu/chemistry/ DepartmentDepartment ofof ChemistryChemistry && BiochemistryBiochemistry Phone: (314) 516-5311 Fax: (314) 516-5342 ST.LOUIS The St. Louis metropolitan region, located around the ence Center has many educational interactive exhibits confluence of the Missouri and Mississippi Rivers, has including an Omnimax theatre. And finally the St. Louis evolved through the centuries from the homes of ancient Zoo, home to more than 18,000 exotic animals, many of Native American civilizations to major fur trading cen- them rare and endangered, and set in the rolling hills, ter to the "Gateway to the West," marked by lasting lakes and glades of Forest Park, is a great place to visit. French, Spanish and African influences. Today the area is a town with hospitable people rooted in a myriad of Activities and attractions are many, and St. Louis has regional, ethnic, and cultural traditions reflective of our a great variety of night life choices. Blues clubs and complex world, well supported by easy access to parks, restaurants are tucked away in the red brick buildings of educational centers, sports venues, museums, and histor- the historic Soulard neighborhood, while Dixieland and ic sites. blues dinner cruises are available through the port of St. Louis. Clubs and restaurants are alive until early morn- Great ethnic and classic neighborhoods characterize ing hours in the converted warehouses of the Landing, the region. A cross-section of the area can provide ex- north of the Arch, and along the newly-developed "loft" amples of wonderful Victorian architecture, museum, neighborhood of Washington Avenue. -
Biodynamo: a New Platform for Large-Scale Biological Simulation
Lukas Johannes Breitwieser, BSc BioDynaMo: A New Platform for Large-Scale Biological Simulation MASTER’S THESIS to achieve the university degree of Diplom-Ingenieur Master’s degree programme Software Engineering and Management submitted to Graz University of Technology Supervisor Ass.Prof. Dipl.-Ing. Dr.techn. Christian Steger Institute for Technical Informatics Advisor Ass.Prof. Dipl.-Ing. Dr.techn. Christian Steger Dr. Fons Rademakers (CERN) November 23, 2016 AFFIDAVIT I declare that I have authored this thesis independently, that I have not used other than the declared sources/resources, and that I have explicitly indicated all ma- terial which has been quoted either literally or by content from the sources used. The text document uploaded to TUGRAZonline is identical to the present master‘s thesis. Date Signature This thesis is dedicated to my parents Monika and Fritz Breitwieser Without their endless love, support and encouragement I would not be where I am today. iii Acknowledgment This thesis would not have been possible without the support of a number of people. I want to thank my supervisor Christian Steger for his guidance, support, and input throughout the creation of this document. Furthermore, I would like to express my deep gratitude towards the entire CERN openlab team, Alberto Di Meglio, Marco Manca and Fons Rademakers for giving me the opportunity to work on this intriguing project. Furthermore, I would like to thank them for vivid discussions, their valuable feedback, scientific freedom and possibility to grow. My gratitude is extended to Roman Bauer from Newcastle University (UK) for his helpful insights about computational biology detailed explanations and valuable feedback. -
CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations
molecules Article CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations 1,2,3, 2,3, 1, 1 Alessandro Marchetto y , Zeineb Si Chaib y , Carlo Alberto Rossi y, Rui Ribeiro , Sergio Pantano 4, Giulia Rossetti 2,5,6,* and Alejandro Giorgetti 1,2,* 1 Department of Biotechnology, University of Verona, 37134 Verona, Italy; [email protected] (A.M.); [email protected] (C.A.R.); [email protected] (R.R.) 2 Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany; [email protected] 3 Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University,52062 Aachen, Germany 4 Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay; [email protected] 5 Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52428 Jülich, Germany 6 Department of Hematology,Oncology,Hemostaseology,and Stem Cell Transplantation, RWTH Aachen University, 52062 Aachen, Germany * Correspondence: [email protected] (G.R.); [email protected] (A.G.) These authors contributed equally to this work. y Academic Editors: Carmen Domene and Mercedes Alfonso-Prieto Received: 30 October 2020; Accepted: 28 November 2020; Published: 15 December 2020 Abstract: Advances in coarse-grained molecular dynamics (CGMD) simulations have extended the use of computational studies on biological macromolecules and their complexes, as well as the interactions of membrane protein and lipid complexes at a reduced level of representation, allowing longer and larger molecular dynamics simulations. Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. -
Marko Leino Process Simulation Unit Operation Models – Review of Open
MARKO LEINO PROCESS SIMULATION UNIT OPERATION MODELS – REVIEW OF OPEN AND HSC CHEMISTRY I/O INTERFACES Master of Science Thesis Examiner: Professor Hannu Jaakkola Examiner and topic approved by the Faculty Council of the Faculty of Business and Built Environment on 6 April 2016 i ABSTRACT MARKO LEINO: Process Simulation Unit Operation Models – Review of Open and HSC Chemistry I/O Interfaces Tampere University of Technology Master of Science Thesis, 76 pages, 29 Appendix pages April 2016 Master’s Degree Programme in Information Technology Major: Software Engineering Examiner: Professor Hannu Jaakkola Keywords: CAPE-OPEN, HSC Chemistry Sim, unit operation, process simulation Chemical process modelling and simulation can be used as a design tool in the development of chemical plants, and is utilized as a means to evaluate different design options. The CAPE- OPEN interface standards were developed to allow the deployment and utilization of process modelling components in any compliant process modelling environment. This thesis examines the possibilities provided by the CAPE-OPEN interfaces and the .NET framework to develop compliant, cross-platform process modelling components, particularly unit operations. From the software engineering point of view, a unit operation is a represen- tation of physical equipment, and contains the mathematical model of its functionality. The study indicates that the differences between the CAPE-OPEN standards and Outotec HSC Chemistry Sim are negligible at the conceptual level. On the other hand, at the implementa- tion level, the differences are quite considerable. Regardless of the simulation application be- ing used, the modelling of unit operations requires interdisciplinary skills, and creating tools and methods to ease the development of such models is well justified. -
Elucidating Binding Sites and Affinities of Erα Agonist and Antagonist to Human Alpha-Fetoprotein by in Silico Modeling and Point Mutagenesis Nurbubu T
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 29 December 2019 doi:10.20944/preprints201912.0374.v1 Peer-reviewed version available at Int. J. Mol. Sci. 2020, 21, 893; doi:10.3390/ijms21030893 Elucidating Binding Sites and Affinities of ERα Agonist and Antagonist to Human Alpha-Fetoprotein by in silico Modeling and Point Mutagenesis Nurbubu T. Moldogazieva1*, Daria S. Ostroverkhova1,2, Nikolai N. Kuzmich1,3, Vladimir V. Kadochnikov4, Alexander A. Terentiev5, Yuri B. Porozov1,4 1 Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University (Sechenov University); Moscow, Russia; 2Department of Bioengineering, M.V. Lomonosov Moscow State University; Moscow, Russia; 3Department of Drug Safety, I.M. Smorodintsev Research Institute of Influenza, WHO National Influenza Centre of Russia; Saint Petersburg, Russia 4Department of Information and Communication Technologies, Saint Petersburg National Research University of Information Technologies, Mechanics and Optics; Saint Petersburg, Russia 5Deparment of Biochemistry and Molecular Biology, N.I. Pirogov Russian National Research Medical University; Moscow Russia *Corresponding author: Nurbubu T. Moldogazieva, e-mail: [email protected] (NM) ¶ These authors contributed equally to this work Short title: Binding of ERα ligands to human alpha-fetoprotein Key words: alpha-fetoprotein, estrogens, selective estrogen receptor modulators, homology-based modeling, molecular docking, protein-ligand interaction, amino acid substitutions. Abbreviations: HAFP, human alpha-fetoprotein; HSA, human serum albumin; E2, 17β-estradiol; DES, diethylstilbestrol. Author contribution: Conceptualization, Nurbubu T. Moldogazieva, Alexander A. Terentiev and Yuri B. Porozov; Data curation, Nurbubu T. Moldogazieva; Formal analysis, Nurbubu T. Moldogazieva and Nikolai N. Kuzmich; Investigation, Daria S. Ostroverkhova and Vladimir V. Kadochnikov; Methodology, Nikolai N. Kuzmich; Supervision, Alexander A. -
Software and Techniques for Bio-Molecular Modelling
Software and Techniques for Bio-Molecular Modelling Azat Mukhametov Published by Austin Publications LLC Published Date: December 01, 2016 Online Edition available at http://austinpublishinggroup.com/ebooks For reprints, please contact us at [email protected] All book chapters are Open Access distributed under the Creative Commons Attribution 4.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of the publication. Upon publication of the eBook, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work, identifying the original source. Statements and opinions expressed in the book are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Software and Techniques for Bio-Molecular Modelling | www.austinpublishinggroup.com/ebooks 1 Copyright Mukhametov A.This book chapter is open access distributed under the Creative Commons Attribution 4.0 International License, which allows users to download, copy and build upon published articles even for com- mercial purposes, as long as the author and publisher are properly credited. We consider to publish more books on the topics of drug design, molecular modelling, and structure-activity relationships.