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BioVEC : A program for Biomolecule Visualization with Ellipsoidal Coarse-graining

BioVEC   |   Images   |   Videos   |   Download  |  Citation

BioVEC is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to berendered as ellipsoids. The use of coarse-graining methods in biomolecular simulation is progressively increasing, mainly to circumvent the current time-scale problem that exists for all-atom molecular dynamics simulations, and to allow for the computational modelling of ever larger systems which address biologically relevant questions. However in spite of this progress, to the authors' knowledge no currently available program allows for the straightforward visualization the dynamics of coarse-grained systems with ellipsoidal constituents.

Partial harpin formation of a block-copolymeric sequence A - T

Above is shown an image of a single stranded DNA forming a partial hairpin.
More examples of images created by BioVEC:
BioVEC running on Windows XP
BioVEC running on Windows XP
Globule formed by single stranded DNA
Globule formed by single stranded DNA
Thermal anisotropy of GM1-pentasaccharide from a complex with the cholera toxin B-pentamer Thermal anisotropy of GM1-pentasaccharide from a complex with the cholera toxin B-pentamer
ANISOU representation of the 1IRO protein ANISOU representation of the 1IRO protein

BioVEC reads in configuration files, which may be output from molecular dynamics simulations that include orientation output in quaternion format, and can render frames of the trajectory in several common image formats for subsequent concatenation into a movie file. Below is shown an example of a single stranded DNA, consisting of two blocks of A and T bases, forming a partial hairpin. The raw simulation data has been averaged over eleven consecutive time steps, to create a smoother animation.

More videos from BioVEC:

AVI movie
(AVI 14MB)
AVI movie
(AVI 14MB)

Download BioVEC

BioVEC was developed by Erik Abrahamsson while in the Plotkin lab. All source codes and documents are released under the GNU General Public License.
Windows:
Precompiled Windows executables
Source code and Dev-C++ Project
Source code and VC++ 2009 Project
Windows C++ Runtime Libraries: msvcr80.dll
Linux:
BioVEC Source code
Additional compilation notes (courtesy of Oriol Vilanova, PhD, U. de Barcelona)
Helper programs:
Smooth.cpp
Manual:
README and documentation
Example files:
Input files for BioVEC
Libraries required to compile BioVEC:
DevIL
GNU Scientific Library
OpenGLUT
FreeGLUT
FreeGLUT for VS 2008
 
C++ Compilers and IDE for Windows:
Dev-C++
Microsoft Visual C++ 2008 Express

BioVEC Citation

Abrahamsson, E. and Plotkin, S. S., ”BioVEC: A program for Biomolecule Visualization with Ellipsoidal Coarse-graining” J. Mol. Graph. Mod. 28, 140-145 (2009) (PDF)

We are pleased to announce that the BioVEC video included in the supplementary materials has won the MGMS Graphics Prize for Best Annual Artwork Submitted to the Journal of Molecular Graphics and Modelling 2010.

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