Treffer: FPV: fast protein visualization using Java 3D.

Title:
FPV: fast protein visualization using Java 3D.
Authors:
Can T; Department of Computer Science, University of California at Santa Barbara, Santa Barbara, CA 93117-5110, USA. tcan@cs.ucsb.edu, Wang Y, Wang YF, Su J
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2003 May 22; Vol. 19 (8), pp. 913-22.
Publication Type:
Comparative Study; Evaluation Study; Journal Article; Research Support, U.S. Gov't, Non-P.H.S.; Validation Study
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Print ISSN: 1367-4803 (Print) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Databases, Protein* , Models, Molecular* , Software*, Information Storage and Retrieval/*methods , Proteins/*chemistry, Computer Graphics ; Computer Simulation ; Computing Methodologies ; Database Management Systems ; Hypermedia ; Imaging, Three-Dimensional/methods ; Internet ; Programming Languages ; Protein Conformation ; Quality Control ; Software Design ; User-Computer Interface
Substance Nomenclature:
0 (Proteins)
Entry Date(s):
Date Created: 20030523 Date Completed: 20030926 Latest Revision: 20191210
Update Code:
20250114
DOI:
10.1093/bioinformatics/btg104
PMID:
12761052
Database:
MEDLINE

Weitere Informationen

Motivation: Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D((TM)) are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison.
Results: In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could.
Availability: EPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/