GPU-powered visualization software and methods with related URL links
This page is an enhanced electronic version of table 1 described in GPU-powered tools boost molecular visualization.
Reference and citation
GPU-powered tools boost molecular visualization
M. Chavent, B. Levy, M. Krone, K. Bidmon, J.P. Nomine, T. Ertl, M. Baaden
Brief Bioinform (2011) doi: 10.1093/bib/bbq089
First published online: February 9, 2011
Illustrations
Table: GPU-powered visualization software and methods with related URL links.
The $ symbol indicates that it is necessary to pay in order to use the program.
| Method/Software | Availability | Cost | OS | Molecular Metaphors | Visual effects | Link to entry |
| Amira | Available | $ | Win, Mac, Linux | Ball and Stick; VdW; Licorice, secondary structures; molecular surface | blur effects | Amira |
| BALLView | Available | Free | Win, Mac, Linux | Ball and Stick; VdW; Licorice; secondary structures; molecular surface | silhouette contouring, cel-shading for 2ndary structure, reflections and shadows | Ballview |
| Chimera | Available | Free | Win, Mac, Linux | Ball and Stick; VdW; Licorice; secondary structures; molecular surface | silhouette contouring | Chimera |
| PMV | Available | Free | Win, Mac, Linux | Ball and Stick; VdW; Licorice; secondary structures; molecular surface | Cel-shading, silhouette contouring | PMV |
| ProteinShader | Available | Free | Win, Mac, Linux | Secondary structures; Ball and Stick; VdW; Licorice | Illustrative rendering | ProteinShader |
| QuteMol | Available | Free | Win, Mac, Linux | Ball and Stick, VdW, Licorice using GPU | ambient occlusion, silhouette contouring, halo | QuteMol |
| TexMol | Available | Free | Win, Mac, Linux | VdW, secondary structures using GPU | - | TexMol |
| VMD | Available | Free | Win, Mac, Linux | VdW using GPU; Ball and Stick; Licorice; secondary structures | - | VMD |
| Yasara | Available | Free | Win, Mac, Linux | Ball and Stick, VdW, Licorice using GPU; secondary structures; molecular surface | ambient occlusion, global shadowing | Yasara |
| Method1: Quadratic Surface primitives | Not available | - | - | Ball and Stick, VDW, Licorice using GPU | global shadowing, silhouette contouring | Method1 |
| Method2:Two-Level approach | Not available | - | - | Ball and Stick, VdW on GPU | silhouette contouring, depth cueing | Method2 |
| Method3:MegaMol: Molecular dynamics visualizations | On request (work in progress) | - | Win, Linux | Molecular Surface on GPU, Secondary structures on CPU-GPU, Ball and Stick using GPU... | transparency, depth cueing, silhouette contouring | Method3 |
| Method4:MetaMol: Molecular Skin Surface | Not available | - | - | Molecular Skin Surface on GPU | crystal effect, HDR rendering | Method4 |
| Method5:Metaballs | Not available | - | - | Metaballs visualization using GPU | silhouette contouring | Method5 |
| Method6:Molecular Surface abstraction | Webserver | Free | - | Simplification of Molecular Surface to keep only representative features | silhouette contouring, ambient occlusion, texture mapping | Method6 |
| Method7:Text scaffold | Not available | - | - | Well suited annotations on molecular surface | - | Method7 |
Visualization software
Amira
Website (Available/$, Win, Mac, Linux)
Metaphors: Ball and Stick; VdW; Licorice, secondary structures; molecular surface
Visual effects: blur effects
BALLView
Website (Available/Free, Win, Mac, Linux)
Metaphors: Ball and Stick; VdW; Licorice; secondary structures; molecular surface
Visual effects: silhouette contouring, cel-shading for 2ndary structure, reflections and shadows
Chimera
Website (Available/Free, Win, Mac, Linux)
Metaphors: Ball and Stick; VdW; Licorice; secondary structures; molecular surface
Visual effects: silhouette contouring
PMV
Website (Available/Free, Win, Mac, Linux)
Metaphors: Ball and Stick; VdW; Licorice; secondary structures; molecular surface
Visual effects: Cel-shading, silhouette contouring
ProteinShader
Website (Available/Free, Win, Mac, Linux)
Metaphors: Secondary structures; Ball and Stick; VdW; Licorice
Visual effects: Illustrative rendering
QuteMol
Website (Available/Free, Win, Mac, Linux)
Metaphors: Ball and Stick, VdW, Licorice using GPU
Visual effects: ambient occlusion, silhouette contouring, halo
TexMol
Website (Available/Free, Win, Mac, Linux)
Metaphors: VdW, secondary structures using GPU
VMD
Website (Available/Free, Win, Mac, Linux)
Metaphors: VdW using GPU; Ball and Stick; Licorice; secondary structures
Yasara
Website (Available/Free, Win, Mac, Linux)
Metaphors: Ball and Stick, VdW, Licorice using GPU; secondary structures; molecular surface
Visual effects: ambient occlusion, global shadowing
Visualization methods
Method1: Quadratic Surface primitives
Video
Metaphors: Ball and Stick, VDW, Licorice using GPU
Visual effects: global shadowing, silhouette contouring
Method2: Two-Level approach
Video
Metaphors: Ball and Stick, VdW on GPU
Visual effects: silhouette contouring, depth cueing
Method3: MegaMol - Molecular dynamics visualizations
Video (On request (work in progress), Win, Linux)
Metaphors: Molecular Surface on GPU, Secondary structures on CPU-GPU, Ball and Stick using GPU...
Visual effects: transparency, depth cueing, silhouette contouring
Method4: MetaMol - Molecular Skin Surface
Video
Metaphors: Molecular Skin Surface on GPU
Visual effects: crystal effect, HDR rendering
Method5: Metaballs
Video
Metaphors: Metaballs visualization using GPU
Visual effects: silhouette contouring
Method6: Molecular Surface abstraction
Video Webserver (Webserver/Free)
Metaphors: Simplification of Molecular Surface to keep only representative features
Visual effects: silhouette contouring, ambient occlusion, texture mapping
Method7: Text scaffold
Video
Metaphors: Well suited annotations on molecular surface
File version:: $Id: gputable1.txt,v 1.5 2011/02/20 14:27:39 marc Exp $
