Molecular graphics

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HaptiMOL

The HaptiMOL suite enables interaction with protein structures using force feedback, through the use of a haptic feedback device:

  • HaptiMOL ISAS enables users to interact with the solvent accessible surface of biomolecules, by probing the surface with a sphere. 
  • HaptiMOL ENM enables users to apply forces to atoms in an elastic network model and to observe the resulting deformation. (A mouse version is also available).
  • HaptiMOL RD (coming soon) will be designed for rigid molecular docking. 
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Institution: University of East Anglia

cellVIEW

cellVIEW is a tool that provides interactive real-time visualization of large biological macromolecular scenes, for instance, depicting bacteria and viruses at atomic resolution. CellVIEW is unique and has been specifically designed to match the ambitions of structural biologist to model and interactively visualize structures comprised of several billions atoms, which corresponds to sizes of small bacterial organisms.

The main purpose of cellVIEW is currently the visualization of the static structures of these microorganisms. We are continuously working on extending cellVIEW's capabilities, for instance in order to allow the depiction of the dynamic machineries of life within these organisms, as well as including modeling capabilities for these nano scale structures.

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Institution: TU Wien

MegaMol

MegaMol™ is a visualization middleware used to visualize point-based molecular datasets.

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Institution: ​Visualization Research Center (VISUS) of the University of Stuttgart, Germany

MegaMol™ is a visualization middleware used to visualize point-based molecular datasets. This software is developed within the Collaborative Research Center 716, subproject D.3 at the Visualization Research Center (VISUS) of the University of Stuttgart and at the Computer Graphics and Visualization Group of the TU Dresden.

BioJS

BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies.

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Institution: BioJS

IBM UKSC history

The IBM United Kingdom Scientific Centre in Winchester over the 1980's had two complementary groups devoted to visualization; graphics and image processing.  We had a strong emphasis on applications, working with various external partners (including Michael Sternberg).  For the graphics group the applications included molecular graphics, archaeology and computer art; the image group was mainly dedicated to medical imaging.  There were a few cross-over projects, for example the creation of a 'beating heart' movie .  The tools we used are no longer available and are included here for historical and archive purposes.

The graphics groups had serveral main tools

  • Winchester Graphics System (WGS) was used for data exploration; it combined relational database technology and interactive 3d graphics with an bridge between the two and scripting.
  • Winchester Solid Modeller (WINSOM) was used for more advanced graphical visualizations.  It combined constructive solid geometry (CSG) with novel methods for blending (e.g. metaballs) and representations of molecular fields.
  • FASTDRAW, which converted the same CSG/field models to polygon for for interactive 3d display.
  • Extensible Solid Model Editor (ESME), for more powerful graphics programming, integrated with generation of WINSOM/FASTDRAW models.

The image processing group had a single tool

  • IAX which incorporated many image processing techniques (some novel) within a simple scriptable framework.  This performed 2d and 3d image analysis, with 3d recognition often passed to Winsom for final display.

The groups had a demonstration prepared for presentation to our visitors.  I have recovered much of this, in particular the still images, and recast it as a web page which is currently available at http://programbits.co.uk/UKSC/uksc.html.  The content was biased toward the graphics group.  Much of the content cannot be displayed, especially the movies (which I hope to preapare in suitable format soon) and the interactive 3d work (which may never be recreated).

The Journal of Molecular Graphics was founded by Andy Morffew, a member of the group;  you may see a disproportionate number of our papers in the early volumes.

Some of the work continues to this day.  William Latham and I are presenting exhibitions of interactive 3d art (one in Norwich in Autumn 2016).  We have a modern version of FASTDRAW (in C#/Unity) which is being used as part of BioBlox, and which I hope to release as open source soon.  There is also a Java version which FoldSynth uses for metaballs.

 

 

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Institution: IBM United Kingdom Scientific Centre

Historical

Molecular Maya

Molecular Maya (mMaya) is a free plugin for Autodesk Maya that lets users import, model and animate molecular structures. We leverage the power and flexibility of Maya while offering innovative, intuitive tools specialized for the challenges of molecular modeling and animation. mMaya is further enhanced by a series of 'kits' that expand its functionality and greatly streamline molecular modeling, animation, and simulation.

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Institution: Digizyme Inc.

GraphiteLifeExplorer

The GraphiteLifeExplorer modeling tool allows to build 3D molecular assemblies of proteins and DNA from Protein Database (PDB) files. Atomic DNA can be modeled from scratch or reconstructed from simulation.

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Institution: Fourmentin-Guilbert Scientific Foundation & Inria

The LifeExplorer initiative aims at providing a multiscale modelisation of a complete bacteria.

One software is currently available: GraphiteLifeExplorer

ParaView

ParaView is an application framework and turnkey application. Users can quickly build visualizations to analyze their data using qualitative and quantitative techniques, with data exploration done interactively in 3D or programmatically using ParaView's batch processing capabilities. Furthermore, the ParaView code base is designed in such a way that all of its components can be reused to quickly develop vertical applications. This flexibility allows ParaView developers to quickly develop applications that have specific functionality for a specific problem domain.

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Institution: Kitware

MembraneEditor

The CELLmicrocosmos 2.2 MembraneEditor can be used to model membranes based on lipid and protein files in PDB format. It is possible to interactively generate structural and compositional heterogeneous membrane patches as well as vesicles. The created structures can be used for visualization purposes, structural analysis or as a base for molecular simulations. Windows, Mac OS X as well as Linux are supported. Requirement: Java 7+ has to be installed beforehand. For semi-automatic placement of proteins, the OPM and PDB_TM database are used. A direct connection to the PDB database for downloading PDB files is also integrated. The PDB export module provides many options, enabling compatibility to all PDB viewers to the best of our knowledge.

Introduction videos you will find here: http://www.cellmicrocosmos.org/index.php/videos

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Institution: University of Konstanz

UCSF Chimera

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use.

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Institution: University of California, San Francisco

Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics, funded by the National Institutes of Health (NIGMS P41-GM103311).

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