iview: an interactive WebGL visualizer for protein-ligand complex

  title={iview: an interactive WebGL visualizer for protein-ligand complex},
  author={Hongjian Li and Kwong-Sak Leung and Takanori Nakane and Man Hon Wong},
  journal={BMC Bioinformatics},
  pages={56 - 56}
BackgroundVisualization of protein-ligand complex plays an important role in elaborating protein-ligand interactions and aiding novel drug design. Most existing web visualizers either rely on slow software rendering, or lack virtual reality support. The vital feature of macromolecular surface construction is also unavailable.ResultsWe have developed iview, an easy-to-use interactive WebGL visualizer of protein-ligand complex. It exploits hardware acceleration rather than software rendering. It… 
Touching proteins with virtual bare hands: how to visualize protein-drug complexes and their dynamics in virtual reality
This work presents a freely available software pipeline for visualising protein structures through VR and has combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-lead drug design by exposing molecular interactions that might be hidden in the less informative static models.
iSyn: WebGL-Based Interactive De Novo Drug Design
iSyn is a WebGL-based tool for interactivede novo drug design that features an evolutionary algorithm that automatically designs novel ligands with drug-like properties and synthetic feasibility using click chemistry and implements a tailor-made interactive visualizer to aid novel drug design.
ProteinVR: Web-based molecular visualization in virtual reality
ProteinVR displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space and is ideal for hypothesis generation and education in research and large-classroom settings.
Touching proteins with virtual bare hands
This work presents a freely available software pipeline for visualising protein structures through VR and combines VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models.
3D-Lab: a collaborative web-based platform for molecular modeling.
The integrated drug-design platform allows drug designers to instantaneously access 3D information and readily apply advanced and automated 3D molecular modeling tasks, with the aim to improve decision-making in drug design projects.
Web3DMol: interactive protein structure visualization based on WebGL
3D modeling program Web3DMol is introduced, a web application focusing on protein structure visualization in modern web browsers that will display and allow interactive manipulation of the 3D structure of proteins in web browsers.
Visualization of molecular structures using state-of-the-art techniques in WebGL
A GPU-based ray-casting technique for the visualization of molecular structures that adheres to the restrictions of WebGL, which shows the potential of establishing the web as an attractive platform for interactive visualization using GPU-accelerated algorithms.
iCn3D, a Web-based 3D Viewer for the Visualization of Biomolecular Structure and Sequence Annotation
iCn3D is unique in its ability to simultaneously show 3D structure, 2D molecular networks and interactions, and 1D protein and nucleotide sequences through an integrated sequence/annotation browser.
BioVR: a platform for virtual reality assisted biological data integration and visualization
BioVR is developed, an easy-to-use interactive, virtual reality (VR)-assisted platform for integrated visual analysis of DNA/RNA/protein sequences and protein structures using Unity3D and the C# programming language, and can be extended to view omics data.


PoseView -- molecular interaction patterns at a glance
PoseView, a tool which displays molecular complexes incorporating a simple, easy-to-perceive arrangement of the ligand and the amino acids towards which it forms interactions, is developed, and the underlying interaction models are presented.
istar: A Web Platform for Large-Scale Protein-Ligand Docking
This work revamped the docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function, and developed a publicly-accessible web platform called istar, which achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed.
GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes
A web server for analyzing protein–small ligand interactions on the basis of patterns of atomic contacts, or “interaction patterns” obtained from the statistical analyses of 3D structures of protein–ligand complexes in a previous study is presented.
Interactive Drug Design in Virtual Reality
An interactive drug design algorithm which generates lead candidates against a protein and compares the quality of resulting ligands between interactive and automatic approaches is presented.
UCSF Chimera—A visualization system for exploratory research and analysis
Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
VMD: visual molecular dynamics.
Visualization methods for molecular studies on the web platform
The proposed technology tries to overcome the standard approach of molecular/biochemical visualization tools, which generally provide a fixed set of visualization methods, by exploiting the capabilities of the WebGL API and the high level objects of the SpiderGL library.
Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform
A new algorithm of EDTSurf is developed for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT).
idock: A multithreaded virtual screening tool for flexible ligand docking
  • Hongjian Li, K. Leung, M. Wong
  • Computer Science
    2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)
  • 2012
AutoDock Vina is a competitive protein-ligand docking tool well known for its fast execution and high accuracy. Nevertheless, when docking a massive number of ligands, Vina has to be run multiple
JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia
JSmol is thus the first full-featured molecular viewer, and the first ever viewer for proteins, which can be utilized with an internet browser on handheld devices lacking Java.