Sim VIZ - A desktop virtual environment for visualization and analysis
of protein multiple simulation trajectories
R. Czekster, and O. de Souza. COMPUTATIONAL SCIENCE AND ITS APPLICATIONS - ICCSA 2006, PT 1, volume 3980 of LECTURE NOTES IN COMPUTER SCIENCE, SPRINGER-VERLAG BERLIN, HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY, (2006)
Abstract
In silico protein conformation simulation generates massive amounts of
data which needs to be properly visualized and analyzed. We are
applying Desktop Information-Rich Virtual Environments (Desktop IRVE's)
techniques and concepts to aid multiple trajectory simulation analysis,
improving user experience and developing a problem-solving environment
to help the decision making process. We will present Sim VIZ, a tool
which integrates visualization to simulation analysis, improving
previous knowledge about trajectories. This environment shows
informative panels, Contact Maps, RMSD charts, the Ramachandran Plot
and a Parallel Coordinate multidimensional visualization of simulation
output in a single rendering scene. Sim VIZ also opens multiple
trajectories along with user associated information concerning many
aspects of the simulation. Sim VIZ is an integrated problem solving
environment of multiple trajectories of protein simulations, offering
various kinds of analysis and visualization tools used by the community
to validate protein structures or to gather a better understanding of
the protein folding process.
%0 Book Section
%1 ISI:000237642900022
%A Czekster, RM
%A de Souza, ON
%B COMPUTATIONAL SCIENCE AND ITS APPLICATIONS - ICCSA 2006, PT 1
%C HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY
%D 2006
%E Gavrilova, M and Gervasi, O and Kumar, V and Tan, CJK and Taniar, D and Lagana, A and Mun, Y and Choo, H,
%I SPRINGER-VERLAG BERLIN
%K 2d RMSD maps visualization
%P 202-211
%T Sim VIZ - A desktop virtual environment for visualization and analysis
of protein multiple simulation trajectories
%V 3980
%X In silico protein conformation simulation generates massive amounts of
data which needs to be properly visualized and analyzed. We are
applying Desktop Information-Rich Virtual Environments (Desktop IRVE's)
techniques and concepts to aid multiple trajectory simulation analysis,
improving user experience and developing a problem-solving environment
to help the decision making process. We will present Sim VIZ, a tool
which integrates visualization to simulation analysis, improving
previous knowledge about trajectories. This environment shows
informative panels, Contact Maps, RMSD charts, the Ramachandran Plot
and a Parallel Coordinate multidimensional visualization of simulation
output in a single rendering scene. Sim VIZ also opens multiple
trajectories along with user associated information concerning many
aspects of the simulation. Sim VIZ is an integrated problem solving
environment of multiple trajectories of protein simulations, offering
various kinds of analysis and visualization tools used by the community
to validate protein structures or to gather a better understanding of
the protein folding process.
%@ 3-540-34070-X
@incollection{ISI:000237642900022,
abstract = {{In silico protein conformation simulation generates massive amounts of
data which needs to be properly visualized and analyzed. We are
applying Desktop Information-Rich Virtual Environments (Desktop IRVE's)
techniques and concepts to aid multiple trajectory simulation analysis,
improving user experience and developing a problem-solving environment
to help the decision making process. We will present Sim VIZ, a tool
which integrates visualization to simulation analysis, improving
previous knowledge about trajectories. This environment shows
informative panels, Contact Maps, RMSD charts, the Ramachandran Plot
and a Parallel Coordinate multidimensional visualization of simulation
output in a single rendering scene. Sim VIZ also opens multiple
trajectories along with user associated information concerning many
aspects of the simulation. Sim VIZ is an integrated problem solving
environment of multiple trajectories of protein simulations, offering
various kinds of analysis and visualization tools used by the community
to validate protein structures or to gather a better understanding of
the protein folding process.}},
added-at = {2009-01-13T23:22:21.000+0100},
address = {{HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY}},
affiliation = {{Czekster, RM (Reprint Author), PUCRS, FACIN, LABIO, PPGCC,Lab Bioinformat Medelagem \& Simulacao Biosi, Av Ipiranga 6681 Predio 16 Sala 106, BR-90619900 Porto Alegre, RS, Brazil.
PUCRS, FACIN, LABIO, PPGCC,Lab Bioinformat Medelagem \& Simulacao Biosi, BR-90619900 Porto Alegre, RS, Brazil.}},
author = {Czekster, RM and de Souza, ON},
author-email = {{osmarns@inf.pucrs.br}},
biburl = {https://www.bibsonomy.org/bibtex/2e85a574f4a562ec918b3d0a116f59c86/huiyangsfsu},
booktitle = {{COMPUTATIONAL SCIENCE AND ITS APPLICATIONS - ICCSA 2006, PT 1}},
cited-references = {{BERMAN HM, 2000, NUCLEIC ACIDS RES, V28, P235.
BOWMAN DA, 2003, VRST 03 P ACM S VIRT, P81.
BRANDEN C, 1999, INTRO PROTEIN STRUCT.
DELANO WL, 2002, PYMOL MOL GRAPHICS S.
FRISHMAN D, 1995, PROTEINS, V23, P566.
FUA YH, 1999, VIS 99 P 10 IEEE VIS.
GUNSTEREN WF, 1990, ANGEW CHEM INT EDIT, V29, P992.
HUMPHREY W, 1996, J MOL GRAPHICS, V14, P33.
INSELBERG A, 1990, P IEEE VIS, P36.
LEACH AR, 2001, MOL MODELING PRINCIP.
MA KL, 2004, COMPUT GRAPHICS-US, V38, P4.
OLIVEIRA MCF, 2003, IEEE T VISUALIZATION, V9, P378.
PEARLMAN DA, 1995, AMBER PACKAGE COMPUT, V9, P1.
POLYS NF, 2004, WEB3D 04 P 9 INT C 3, P7.
POLYS NF, 2005, VIRTUAL REALITY, V8, P41.
RIBARSKY W, 1994, COMPUTER, V27, P57.
SHNEIDERMAN B, 1996, VL 96 P 1996 IEEE S, P336.
VAILAYA A, 2005, BIOINFORMATICS, V21, P430, DOI 10.1093/bioinformatics/bti187.
VANGUNSTEREN WF, 1998, J CHEM PHYS, V108, P6109.
VANTEYLINGEN R, 1997, IEEE T VIS COMPUT GR, V3, P65.
VENDRUSCOLO M, 1998, FOLD DES, V3, P329.
WARD MO, 2002, INFORMATION VISUALIZ, V1, P194.
WARE C, 2000, INFORM VISUALIZATION.}},
doc-delivery-number = {{BEK99}},
editor = {{Gavrilova, M and Gervasi, O and Kumar, V and Tan, CJK and Taniar, D and Lagana, A and Mun, Y and Choo, H}},
interhash = {cce150d4f39a903790c1569465ccd5b5},
intrahash = {e85a574f4a562ec918b3d0a116f59c86},
isbn = {{3-540-34070-X}},
issn = {{0302-9743}},
keywords = {2d RMSD maps visualization},
keywords-plus = {{MOLECULAR-DYNAMICS}},
language = {{English}},
number-of-cited-references = {{23}},
pages = {{202-211}},
publisher = {{SPRINGER-VERLAG BERLIN}},
series = {{LECTURE NOTES IN COMPUTER SCIENCE}},
subject-category = {{Computer Science, Theory \& Methods}},
times-cited = {{0}},
timestamp = {2009-01-13T23:22:21.000+0100},
title = {{Sim VIZ - A desktop virtual environment for visualization and analysis
of protein multiple simulation trajectories}},
type = {{Proceedings Paper}},
unique-id = {{ISI:000237642900022}},
volume = {{3980}},
year = {{2006}}
}