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NGL Viewer: a web application for molecular visualization

Alexander S. Rose, Peter W. Hildebrand
2015 Nucleic Acids Research  
By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of  ...  Generally, the web application offers comprehensive molecular visualization through a graphical user interface so that life scientists can easily access and profit from available structural data.  ...  ACKNOWLEDGEMENT We thank Heiko Bittner, Johanna Tiemann and Jochen Ismer for testing the software and suggesting features.  ... 
doi:10.1093/nar/gkv402 pmid:25925569 pmcid:PMC4489237 fatcat:tkjacmsrabhcblzvhwndznml4i

ENBIK2018 - Mol* - Towards a common library and tools for web molecular graphics.pdf [article]

Alexander Rose, David Sehnal, Jaroslav Koča, Sameer Velankar, Stephen Burley
2018 Figshare  
Web-browser based visualization and analysis of macromolecular structures and associated data represents a crucial step in gaining knowledge from these data.  ...  representation of molecular assemblies).  ...  Acknowledgments/Funding Thank you for your attention RCSB PDB is funded by NSF, NIH, DOE  ... 
doi:10.6084/m9.figshare.6541235 fatcat:igrio2rbgbc2zpxjh77kfrrici

Concept of a Cloud Service for Data Preparation and Computational Control on Custom HPC Systems in Application to Molecular Dynamics

Dmitry Puzyrkov, Sergey Polyakov, Viktoriia Podryga, Sergey Markizov, Gh. Adam, J. Buša, M. Hnatič, D. Podgainy
2018 EPJ Web of Conferences  
The paper describes the prototype of a cloud service, intended for design of atomistic systems of large volume for further detailed molecular dynamic calculations and computational management for this  ...  At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics  ...  CAD-application The graphical geometry designer is a CAD-like web application using WebGL (Web Graphics Library) for drawing a three-dimensional design area.  ... 
doi:10.1051/epjconf/201817305014 fatcat:a3wjgm7muvderf3mgiwlun7b4a

Genomic pathways database and biological data management

Z. M. Ozsoyoglu, G. Ozsoyoglu, J. Nadeau
2006 Animal Genetics  
outputs, and, (e) an implementation that allows for web(XML)-based dissemination of query outputs (i.e., pathways data in BIOPAX format) to researchers in the community, giving them control on the use  ...  PathCase is an integrated set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal  ...  The web-based PathCase version is built around two subsystems, namely, the PathCase Server and the PathCase Web Client.  ... 
doi:10.1111/j.1365-2052.2006.01477.x pmid:16887001 fatcat:v3uph3nkyvbmvdennnpfkrecsy

NaviCell Web Service for network-based data visualization

Eric Bonnet, Eric Viara, Inna Kuperstein, Laurence Calzone, David P. A. Cohen, Emmanuel Barillot, Andrei Zinovyev
2015 Nucleic Acids Research  
NaviCell Web Service is a tool for network-based visualization of 'omics' data which implements several data visual representation methods and utilities for combining them together.  ...  Nav-iCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of  ...  ACKNOWLEDGEMENTS We thank Christophe Russo for preparing the mutation data and Tatiana Popova for helping with ovarian TCGA dataset.  ... 
doi:10.1093/nar/gkv450 pmid:25958393 pmcid:PMC4489283 fatcat:f64zxz4svzeexhr7kd3hjb6wuu

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose
2021 Nucleic Acids Research  
High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level  ...  The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological  ...  ACKNOWLEDGEMENTS We wish to thank Dr Ludovic Autin for his contributions to the cellPACK support, Aron Kovacs for improvements in 3D rendering, Dr Daniel Smith for help with molecular orbitals rendering  ... 
doi:10.1093/nar/gkab314 pmid:33956157 pmcid:PMC8262734 fatcat:zwxfdrql6fdarhjcmw7wv4rvaq

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura
2016 Nucleic Acids Research  
Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.  ...  We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former.  ...  Kudou for technical support.  ... 
doi:10.1093/nar/gkw962 pmid:27789697 pmcid:PMC5210648 fatcat:pan6qdrpe5bknfgkot6blgnp6u

3Dmol.js: molecular visualization with WebGL

N. Rego, D. Koes
2014 Bioinformatics  
3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the  ...  need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in  ...  Acknowledgements We are grateful to Takanori Nakane for creating GLmol. We would also like to thank Caleb Martin for his contributions.  ... 
doi:10.1093/bioinformatics/btu829 pmid:25505090 pmcid:PMC4393526 fatcat:xkbofqsm6vdjncukh3j44zbgze

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics

Melanie C Burger
2015 Journal of Cheminformatics  
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  ...  The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms.  ...  Acknowledgements MB would like to thank CIHR and the Vesalius Trust for funding Lab 3 D development, and iChemLabs for being available to answer questions during the preparation of the manuscript.  ... 
doi:10.1186/s13321-015-0085-3 pmid:26185528 pmcid:PMC4503857 fatcat:v634zecygja4ffnakxtmqhd3ny

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Inna Kuperstein, David PA Cohen, Stuart Pook, Eric Viara, Laurence Calzone, Emmanuel Barillot, Andrei Zinovyev
2013 BMC Systems Biology  
Results: NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance.  ...  map and (3) integrated web-based blog for collecting community feedback.  ...  Acknowledgments We thank Camille Barette for help in setting up the informatics recourses and Hien-Anh Nuigen for help with NaviCell guides design. This work is  ... 
doi:10.1186/1752-0509-7-100 pmid:24099179 pmcid:PMC3851986 fatcat:haermrxsobeoji27kppru5eedq

BIND--The Biomolecular Interaction Network Database

G. D. Bader
2001 Nucleic Acids Research  
BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid  ...  We have developed a new graphical analysis tool that provides users with a view of the domain composition of proteins in interaction and complex records to help relate functional domains to protein interactions  ...  molecular complex records and colleagues in the Hogue lab and at the SLRI for helpful discussions.  ... 
doi:10.1093/nar/29.1.242 pmid:11125103 pmcid:PMC29820 fatcat:jd4hd2kuwrhv5ffywzia6psat4

BIND: the Biomolecular Interaction Network Database

G. D. Bader
2003 Nucleic Acids Research  
BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid  ...  We have developed a new graphical analysis tool that provides users with a view of the domain composition of proteins in interaction and complex records to help relate functional domains to protein interactions  ...  molecular complex records and colleagues in the Hogue lab and at the SLRI for helpful discussions.  ... 
doi:10.1093/nar/gkg056 pmid:12519993 pmcid:PMC165503 fatcat:uffhsjhp7netldhopd26f3etkq

Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers

Luciano A. Abriata
2020 PeerJ Computer Science  
Here, I discuss building blocks for creating marker-based AR applications that run as web pages on regular computers, and explore how they can be exploited to develop web content for handling virtual molecular  ...  For years, immersive interfaces using virtual and augmented reality (AR) for molecular visualization and modeling have promised a revolution in the way how we teach, learn, communicate and work in chemistry  ...  ADDITIONAL INFORMATION AND DECLARATIONS Funding The author received no funding for this work.  ... 
doi:10.7717/peerj-cs.260 pmid:33816912 pmcid:PMC7924717 fatcat:2uoto3ahbrbzrmxixvzf6o2oaa

Web Apps Come of Age for Molecular Sciences

Luciano Abriata
2017 Informatics  
Through examples based on JavaScript libraries, web applets, and even full web apps, either alone or coupled to each other, the article puts on the spotlight the potential of these technologies for carrying  ...  This article reviews the best-established tools for in-browser plugin-less programming, including JavaScript as used in HTML5 as well as related web technologies.  ...  Some unreferenced web apps of direct use in molecular biosciences, that rely entirely or largely on JavaScript.  ... 
doi:10.3390/informatics4030028 fatcat:xrz2ijpkdzfjfna43x6nexocam

Modern Scientific Visualizations on the Web

Loraine Franke, Daniel Haehn
2020 Informatics  
Modern scientific visualization is web-based and uses emerging technology such as WebGL (Web Graphics Library) and WebGPU (Web Graphical Processing Unit)for three-dimensional computer graphics and WebXR  ...  We review the state-of-the-art of web-based scientific visualization and present an overview of existing methods categorized by application domain.  ...  [17] present a web-based visualization for dynamic molecular data based on WebGL GPU-based raycasting where each sphere represents an atom [17] .  ... 
doi:10.3390/informatics7040037 fatcat:2xfkzuv4ybdw3hxzn5ym7slgsa
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