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

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.

BioVEC running on Windows XP	Globule formed by single stranded DNA
Thermal anisotropy of GM1-pentasaccharide from a complex with the cholera toxin B-pentamer	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 14MB)

(AVI 14MB)

Download BioVEC

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.