Last updated: 29 April 2009.
About
Bodil is a modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing. Functionality of Bodil is implemented in dynamically loaded modules. Most of the modules available in the present release provide visualization tools, with protein modeling, small-molecule ligand docking and other modules being currently under development. New modules can easily be added via a documented C++ application programming interface.
Bodil is written in standard C++ using the Qt application development framework and OpenGL 3D graphics. The software has been ported to Linux, SGI Irix and Microsoft Windows NT/2000/XP platforms.
Bibliographic reference
Please cite:
Lehtonen JV, Still DJ, Rantanen VV, Ekholm J, Björklund D, Iftikhar Z, Huhtala M, Repo S, Jussila A, Jaakkola J, Pentikäinen O, Nyrönen T, Salminen T, Gyllenberg M and Johnson M. BODIL: a molecular modeling environment for structure-function analysis and drug design. J Comput Aided Mol Des 2004 Jun;18(6):401-419.
In BibTeX format:
@Article{pmid15663001,
author = {Lehtonen, Jukka V. and Still, Dan-Johan and
Rantanen, Ville-Veikko and Ekholm, Jan and
Bj{\"o}rklund, Dag and Iftikhar, Zuhair and Huhtala,
Mikko and Repo, Susanna and Jussila, Antti and
Jaakkola, Jussi and Pentik{\"a}inen, Olli and
Nyr{\"o}nen, Tommi and Salminen, Tiina and
Gyllenberg, Mats and Johnson, Mark S.},
title = {{BODIL}: a molecular modeling environment for
structure-function analysis and drug design},
journal = {J Comput Aided Mol Des},
year = 2004,
volume = 18,
number = 6,
pages = {401--419},
Month = jun
}
Acknowledgements
Bodil is a result of the collective effort of the following individuals during the period 1998-2005:
Åbo Akademi University, Department of Biochemistry and Pharmacy
- Jukka Lehtonen, Ph.D.
- Dag Björklund, M.Sc.
- Jan Ekholm, M.Sc.
- Zuhair Iftikhar, M.Sc.
- Antti Jussila, M.Sc.
- Dan-Johan Still, M.Sc.
- Susanna Repo, M.Sc.
- Professor Mark S. Johnson
University of Turku, Department of Mathematics
- Ville-Veikko Rantanen, Ph.D.
- Jussi Jaakkola, M.Sc.
- Professor Mats Gyllenberg
The development of Bodil was made possible by funding from: the Technology Development Center of Finland (TEKES), the Academy of Finland, the Erna and Victor Hasselblad Foundation, Åbo Akademi University, the Center for Scientific Computing, Fatman Bioinformational Designs Ltd., the National Graduate School in Informational and Structural Biochemistry (ISB) and the Graduate School in Computational Biology, Bioinformatics and Biometry (COMBI).
We are grateful for constructive feedback and encouragement from members of the Structural Bioinformatics Laboratory at the Department of Biochemistry and Pharmacy, Åbo Akademi University, and in particular, Olli Pentikäinen.