Visualizing 3D Molecular Structures Using an Augmented Reality App
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Open Data, Open Source, and Open Standards in Chemistry: the Blue Obelisk Five Years On" Journal of Cheminformatics Vol
Oral Roberts University Digital Showcase College of Science and Engineering Faculty College of Science and Engineering Research and Scholarship 10-14-2011 Open Data, Open Source, and Open Standards in Chemistry: The lueB Obelisk five years on Andrew Lang Noel M. O'Boyle Rajarshi Guha National Institutes of Health Egon Willighagen Maastricht University Samuel Adams See next page for additional authors Follow this and additional works at: http://digitalshowcase.oru.edu/cose_pub Part of the Chemistry Commons Recommended Citation Andrew Lang, Noel M O'Boyle, Rajarshi Guha, Egon Willighagen, et al.. "Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on" Journal of Cheminformatics Vol. 3 Iss. 37 (2011) Available at: http://works.bepress.com/andrew-sid-lang/ 19/ This Article is brought to you for free and open access by the College of Science and Engineering at Digital Showcase. It has been accepted for inclusion in College of Science and Engineering Faculty Research and Scholarship by an authorized administrator of Digital Showcase. For more information, please contact [email protected]. Authors Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean- Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, and Peter Murray-Rust This article is available at Digital Showcase: http://digitalshowcase.oru.edu/cose_pub/34 Oral Roberts University From the SelectedWorks of Andrew Lang October 14, 2011 Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on Andrew Lang Noel M O'Boyle Rajarshi Guha, National Institutes of Health Egon Willighagen, Maastricht University Samuel Adams, et al. -
A Web-Based 3D Molecular Structure Editor and Visualizer Platform
Mohebifar and Sajadi J Cheminform (2015) 7:56 DOI 10.1186/s13321-015-0101-7 SOFTWARE Open Access Chemozart: a web‑based 3D molecular structure editor and visualizer platform Mohamad Mohebifar* and Fatemehsadat Sajadi Abstract Background: Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimen- sional structures of molecules. Results: With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user- friendly interface is composed. More than 30 packages are used to compose this application which adds enough flex- ibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Conclusions: Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (applica- tion programming interface). JavaScript libraries which allow creation of web pages containing interactive three- dimensional molecular structures has also been made available. -
Getting Started in Jmol
Getting Started in Jmol Part of the Jmol Training Guide from the MSOE Center for BioMolecular Modeling Interactive version available at http://cbm.msoe.edu/teachingResources/jmol/jmolTraining/started.html Introduction Physical models of proteins are powerful tools that can be used synergistically with computer visualizations to explore protein structure and function. Although it is interesting to explore models and visualizations created by others, it is much more engaging to create your own! At the MSOE Center for BioMolecular Modeling we use the molecular visualization program Jmol to explore protein and molecular structures in fully interactive 3-dimensional displays. Jmol a free, open source molecular visualization program used by students, educators and researchers internationally. The Jmol Training Guide from the MSOE Center for BioMolecular Modeling will provide the tools needed to create molecular renderings, physical models using 3-D printing technologies, as well as Jmol animations for online tutorials or electronic posters. Examples of Proteins in Jmol Jmol allows users to rotate proteins and molecular structures in a fully interactive 3-dimensional display. Some sample proteins designed with Jmol are shown to the right. Hemoglobin Proteins Insulin Proteins Green Fluorescent safely carry oxygen in the help regulate sugar in Proteins create blood. the bloodstream. bioluminescence in animals like jellyfish. Downloading Jmol Jmol Can be Used in Two Ways: 1. As an independent program on a desktop - Jmol can be downloaded to run on your desktop like any other program. It uses a Java platform and therefore functions equally well in a PC or Mac environment. 2. As a web application - Jmol has a web-based version (oftern refered to as "JSmol") that runs on a JavaScript platform and therefore functions equally well on all HTML5 compatible browsers such as Firefox, Internet Explorer, Safari and Chrome. -
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department Name of FOSS Applications Employability GChemPaint GChemPaint is an editor for 2Dchem- GChemPaint is currently being developed ical structures with a multiple docu- as part of The Chemistry Development ment interface. Kit, and a Standard Widget Tool kit- based GChemPaint application is being developed, as part of Bioclipse. Jmol Jmol applet is used to explore the Jmol is a free, open source molecule viewer structure of molecules. Jmol applet is for students, educators, and researchers used to depict X-ray structures in chemistry and biochemistry. It is cross- platform, running on Windows, Mac OS X, and Linux/Unix systems. For PG Students LaTeX Document markup language and Value addition to academic Skills set. preparation system for Tex typesetting Essential for International paper presentation and scientific journals. For PG student for their project work Scilab Scientific Computation package for Value addition in technical problem numerical computations solving via use of computational methods for engineering problems, Applicable in Chemical, ECE, Electrical, Electronics, Civil, Mechanical, Mathematics etc. For PG student who are taking Physical Chemistry Avogadro Avogadro is a free and open source, Research and Development in Chemistry, advanced molecule editor and Pharmacist and University lecturers. visualizer designed for cross-platform use in computational chemistry, molecular modeling, material science, bioinformatics, etc. Spoken Tutorial Project, IIT Bombay Brochure for Commerce and Commerce IT Name of FOSS Applications / Employability LibreOffice – Writer, Calc, Writing letters, documents, creating spreadsheets, tables, Impress making presentations, desktop publishing LibreOffice – Base, Draw, Managing databases, Drawing, doing simple Mathematical Math operations For Commerce IT Students Drupal Drupal is a free and open source content management system (CMS). -
Designing Universal Chemical Markup (UCM) Through the Reusable Methodology Based on Analyzing Existing Related Formats
Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats Background: In order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data. While the new format is discussed more in the next article, here we describe our software s t tools and two stage analysis procedure that supplied the necessary information for the n i r development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, P CTfile and XDfile. In addition the following formats were included in the first stage only: e r P CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2. Results: A two stage analysis process devised for both XML (Extensible Markup Language) and non-XML formats enabled us to verify if and how potential advantages of XML are utilized in the widely used general-purpose chemical formats. In the first stage we accumulated information about analyzed formats and selected the formats with the most general-purpose chemical functionality for the second stage. During the second stage our set of software quality requirements was used to assess the benefits and issues of selected formats. Additionally, the detailed analysis of XML formats structure in the second stage helped us to identify concepts in those formats. Using these concepts we came up with the concise structure for a new chemical format, which is designed to provide precise built-in validation capabilities and aims to avoid the potential issues of analyzed formats. -
Notes on OLEX2
Notes on OLEX2 Updated on 12 January 2018,at 09:05. Olex2 v1.2-dev © OlexSys Ltd. 2004 – 2016 Compilation Info: 2017.07.20 svn.r3457 MSC:150030729 on WIN64, Python: 2.7.5, wxWidgets: 3.1.0 for OlexSys Ilia A. Guzei 2124 Chemistry Department, University of Wisconsin-Madison, 1101 University Ave, Madison, WI 53706 USA. This is work in progress. You are encouraged to e-mail me ([email protected]) your comments, corrections, and suggestions. Many thanks to Nattamai Bhuvanesh, Brian Dolinar, Oleg Dolomanov, Dean Johnston, Horst Puschmann, Amy Sarjeant, Charlotte Stern, for proof- reading, suggestions, and comments. I have also borrowed from Martin Lutz, Len Barbour, Richard Staples and Tony Linden. OLEX2 Manual Table of Content Table of Content ........................................................................................................................... 2 How to install OLEX2 under Windows .......................................................................................... 3 How to install OLEX2 on a Mac .................................................................................................... 6 Installing and using PLATON on a Mac ........................................................................................ 8 How to get OLEX2 to use PLATON ............................................................................................ 11 About program OLEX2 ................................................................................................................ 11 Keyboard shortcuts ..................................................................................................................... -
Open Data, Open Source and Open Standards in Chemistry: the Blue Obelisk five Years On
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk ¯ve years on Noel M O'Boyle¤1 , Rajarshi Guha2 , Egon L Willighagen3 , Samuel E Adams4 , Jonathan Alvarsson5 , Richard L Apodaca6 , Jean-Claude Bradley7 , Igor V Filippov8 , Robert M Hanson9 , Marcus D Hanwell10 , Geo®rey R Hutchison11 , Craig A James12 , Nina Jeliazkova13 , Andrew SID Lang14 , Karol M Langner15 , David C Lonie16 , Daniel M Lowe4 , J¶er^omePansanel17 , Dmitry Pavlov18 , Ola Spjuth5 , Christoph Steinbeck19 , Adam L Tenderholt20 , Kevin J Theisen21 , Peter Murray-Rust4 1Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, College Road, Cork, Co. Cork, Ireland 2NIH Center for Translational Therapeutics, 9800 Medical Center Drive, Rockville, MD 20878, USA 3Division of Molecular Toxicology, Institute of Environmental Medicine, Nobels vaeg 13, Karolinska Institutet, 171 77 Stockholm, Sweden 4Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Lens¯eld Road, CB2 1EW, UK 5Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden 6Metamolecular, LLC, 8070 La Jolla Shores Drive #464, La Jolla, CA 92037, USA 7Department of Chemistry, Drexel University, 32nd and Chestnut streets, Philadelphia, PA 19104, USA 8Chemical Biology Laboratory, Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA 9St. Olaf College, 1520 St. Olaf Ave., North¯eld, MN 55057, USA 10Kitware, Inc., 28 Corporate Drive, Clifton Park, NY 12065, USA 11Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA 12eMolecules Inc., 380 Stevens Ave., Solana Beach, California 92075, USA 13Ideaconsult Ltd., 4.A.Kanchev str., So¯a 1000, Bulgaria 14Department of Engineering, Computer Science, Physics, and Mathematics, Oral Roberts University, 7777 S. -
3D-Printing Models for Chemistry
3D-Printing Models for Chemistry: A Step-by-Step Open-Source Guide for Hobbyists, Corporate ProfessionAls, and Educators and Student in K-12 and Higher Education Poster Elisabeth Grace Billman-Benveniste+, Jacob Franz++, Loredana Valenzano-Slough+* +Department of Chemistry, Michigan Technological University, ++Department of Mechanical Engineering, Michigan Technological University *Corresponding Author References 1. “LulzBot TAZ 5.” LulzBot, 14 Aug. 2018, www.lulzbot.com/store/printers/lulzbot-taz-5 2. Gaussian 16, Revision B.01, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.; Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, D.; ZakrzeWski, V. G.; Gao, J.; Rega, N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; HasegaWa, J.; Ishida, M.; NakaJima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J. Gaussian, Inc., Wallingford CT, 2016. 3. -
Chemdoodle Web Components: HTML5 Toolkit for Chemical Graphics, Interfaces, and Informatics Melanie C Burger1,2*
Burger. J Cheminform (2015) 7:35 DOI 10.1186/s13321-015-0085-3 REVIEW Open Access ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics Melanie C Burger1,2* Abstract ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses <canvas> and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochem- istry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses. Keywords: ChemDoodle Web Components, Chemical graphics, Animations, Cheminformatics, HTML5, Canvas, JavaScript, WebGL, Structure editor, Structure query Introduction Mobile browsers did support HTML5, which opened How we communicate chemical information is increas- the door to web applications built with only HTML, ingly technology driven. Learning management systems, CSS and JavaScript (JS), such as the ChemDoodle Web virtual classrooms and MOOCs are a few examples where Components. chemistry educators need forward compatible tools for digital natives. Companies that implement emerg- Review ing web technologies can find efficiencies and benefit The ChemDoodle Web Components technology stack from competitive advantages. The first chemical graph- and features ics toolkit for the web, MDL Chime, was introduced in The ChemDoodle Web Components library, released in 1996 [1]. Based on the molecular visualization program 2009, is the first chemistry toolkit for structure viewing RasMol, Chime was developed as a plugin for Netscape and editing that is originally built using only web stand- and later for Internet Explorer and Firefox. -
Development and Application of a Computational Platform for Complex Molecular Design Jaime Rodríguez-Guerra Pedregal
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Development and Application of a Computational Platform for Complex Molecular Design a dissertation submitted by Jaime Rodríguez-Guerra Pedregal & directed by Prof. Dr. Jean-Didier Maréchal in fulfillment of the requirements for the degree of Doctor of Biotechnology Tutor: Prof. Dr. Jordi Joan Cairó Badillo Department of Chemical, Biological and Environmental Engineering Universitat Autònoma de Barcelona July 2018 Development and Application of a Computational Platform for Complex Molecular Design a dissertation submitted by & recommended for acceptance by advisor Jaime Rodríguez-Guerra Pedregal Prof. Dr. Jean-Didier Maréchal Tutor: Prof. Dr. Jordi Joan Cairó Badillo Department of Chemical, Biological and Environmental Engineering Universitat Autònoma de Barcelona July 2018 ©2018 – Jaime Rodríguez-Guerra Pedregal Licensed as Creative Commons BY-NC-ND Attribution-NonCommercial-NoDerivs In the beginning, there was nothing. And God said «Let there be light». And there was light. There was still nothing, but you could see it a lot better. —WoodyAllen. Development and Application of a Computational Platform for Complex Molecular Design by Jaime Rodríguez-Guerra Pedregal Abstract In this dissertation, a series of novel computational modeling tools is reported. -
Page 1 of 52 RSC Advances
RSC Advances This is an Accepted Manuscript, which has been through the Royal Society of Chemistry peer review process and has been accepted for publication. Accepted Manuscripts are published online shortly after acceptance, before technical editing, formatting and proof reading. Using this free service, authors can make their results available to the community, in citable form, before we publish the edited article. This Accepted Manuscript will be replaced by the edited, formatted and paginated article as soon as this is available. You can find more information about Accepted Manuscripts in the Information for Authors. Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal’s standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains. www.rsc.org/advances Page 1 of 52 RSC Advances Synthesis, DNA/protein binding, molecular docking, DNA cleavage and in vitro anticancer activity of nickel(II) bis(thiosemicarbazone) complexes Jebiti Haribabu,a Kumaramangalam Jeyalakshmi, a Yuvaraj Arun, b Nattamai S. P. Bhuvanesh, c Paramasivan Thirumalai Perumal, b and Ramasamy Karvembu a* Abstract A series of N-substituted isatin thiosemicarbazone ligands (L1-L5) and their nickel(II) complexes [Ni(L)2] ( 1-5) were synthesized and characterized by elemental analyses and UV- Visible, FT-IR, 1H & 13 C NMR, and mass spectroscopic techniques. The molecular structure of ligands (L1 and L2) and complex 1 was confirmed by single crystal X-ray crystallography. -
Open Chemoinformatic Resources to Explore the Structure, Properties and Chemical Space of Cite This: RSC Adv.,2017,7,54153 Molecules
RSC Advances REVIEW View Article Online View Journal | View Issue Open chemoinformatic resources to explore the structure, properties and chemical space of Cite this: RSC Adv.,2017,7,54153 molecules a ab a Mariana Gonzalez-Medina,´ J. Jesus´ Naveja, Norberto Sanchez-Cruz´ a and Jose´ L. Medina-Franco * New technologies are shaping the way drug discovery data is analyzed and shared. Open data initiatives and web servers are assisting the analysis of the large amounts of data that we are now able to produce. The final goal is to accelerate the process of moving from new data to useful information that could lead to Received 27th October 2017 treatments for human diseases. This review discusses open chemoinformatic resources to analyze the Accepted 21st November 2017 diversity and coverage of the chemical space of screening libraries and to explore structure–activity DOI: 10.1039/c7ra11831g relationships of screening data sets. Free resources to implement workflows and representative web- rsc.li/rsc-advances based applications are emphasized. Future directions in this field are also discussed. Creative Commons Attribution 3.0 Unported Licence. 1. Introduction connections between biological activities, ligands and proteins.3 During the past few years, there has been an important increase Herein we review representative chemoinformatic tools in open data initiatives to promote the availability of free essential to explore the structure, chemical space and properties research-based tools and information.1 While there is still some of molecules. The review is focused on recent and representative resistance to open data in some chemistry and drug discovery free web-based applications.