abstract

Web-based molecular graphics for large complexes

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Peter W. RoseAuthors Info & Claims

Web3D '16: Proceedings of the 21st International Conference on Web3D Technology

Pages 185 - 186

https://doi.org/10.1145/2945292.2945324

Published: 22 July 2016 Publication History

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Abstract

The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental techniques advance at an unprecedented rate and deliver structures of increasing size. We have tackled this problem by introducing the binary and compressed Macromolecular Transmission Format (MMTF) to reduce network transfer and parsing time, and by developing NGL, a highly memory-efficient and scalable WebGL-based viewer. MMTF offers over 75% compression over the standard mmCIF format, is over an order of magnitude faster to parse, and contains additional information (e.g., bond information). NGL renders molecular complexes with millions of atoms interactively on desktop computers and smartphones alike, making it a tool of choice for web-based molecular visualization in research and education.

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Rose, A. S., and Hildebrand, P. W. 2015. NGL Viewer: a web application for molecular visualization. In Nucleic Acids Research 43:W576--9.

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Rose, P. W., Prlic, A., Bi, C., Bluhm, W. F., Christie, C. H., Dutta, S., Green, R. K., Goodsell, D. S., Westbrook, J. D., Woo, J., Young, J., Zardecki, C., Berman, H. M., Bourne, P. E., Burley, S. K. 2015. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. In Nucleic Acids Research. 43:D345--56.

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Zareei SKhorsand BDantism AZareei NAsgharzadeh FZahraee SMashreghi Kashan SHekmatirad SAmini SGhasemi FMoradnia MVaghf AHemmatpour AHourfar HNiknia SJohari ASalimi FFariborzi NShojaei ZAsiaei EShabani H(2024)PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discoveryDatabase10.1093/database/baae0922024Online publication date: 20-Sep-2024
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Bayne ADong JAmiri SFarhan STrempe J(2023)MTSviewer: A database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structuresPLOS ONE10.1371/journal.pone.028454118:4(e0284541)Online publication date: 24-Apr-2023
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Tam JChua AGallagher AOmene DOkun DDiFranzo DChen BWang MYoon B(2023)A Containerization Framework for Bioinformatics Software to Advance Scalability, Portability, and MaintainabilityProceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/3584371.3612948(1-5)Online publication date: 3-Sep-2023
https://dl.acm.org/doi/10.1145/3584371.3612948
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Index Terms

Web-based molecular graphics for large complexes
1. Human-centered computing
  1. Visualization
    1. Visualization application domains
      1. Scientific visualization

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Web3D '16: Proceedings of the 21st International Conference on Web3D Technology

July 2016

173 pages

ISBN:9781450344289

DOI:10.1145/2945292

Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

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Association for Computing Machinery

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Published: 22 July 2016

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National Institutes of Health

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SIGGRAPH

Web3D '16: The 21st International Conference on Web3D Technology

July 22 - 24, 2016

California, Anaheim

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Collaborative and Parallelized Immersive Molecular Docking

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Collaborative and Parallelized Immersive Molecular Docking

Visualization of molecular structures using state-of-the-art techniques in WebGL

Visual Haptic-Based Biomolecular Docking and Its Applications in E-Learning

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