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DSMM - a Database of Simulated Molecular Motions


NAR Molecular Biology Database Collection entry number 386
Finocchiaro, G.2, Wang, T.1, Hoffmann, R.1, Gonzalez, A.1, Wade, R.C.1
1European Media Laboratory, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany
2European Molecular Biology Laboratory, Meyerhofstr. 1, 69012 Heidelberg, Germany

Database Description

DSMM is a Database of Simulated Molecular Motions. This database is designed to serve as a single searchable site for locating movies and animations from simulations of biomolecules. DSMM is accessible via a webserver at: http://projects.villa-bosch.de/dbase/dsmm/. Many molecular modeling and simulation studies have contributed to our understanding of biomolecular dynamics. Movies of trajectories from molecular simulations and animations consisting of concatenated snapshots of molecules provide a valuable means to visualize the results of such studies. They are insightful in the research context and a useful teaching aid in the classroom. Such movies often summarize the results of many CPU hours of simulation. However, they are rarely to be found in the final published results. Instead, many authors put their movies on their own web pages. This means that it is not easy to find out which movies are available, and searching for particular movies is a somewhat haphazard and unreliable process. Consequently, we decided to build a web-accessible database, DSMM, which would store information on molecular movies at a single location where they could be easily searched and located. All movies collected in DSMM are results from simulations including molecular dynamics, Brownian dynamics, docking, energy minimization, NMR refinement and QM/MM calculations. Some of these simulations are run with the aim of obtaining a realistic picture of the dynamics of molecules as a function of time. In other cases, simulation techniques are used to derive specific information related to molecular function, such as low energy conformations or thermodynamic quantities. In the latter cases, movies can illuminate certain aspects of a molecule's function or how a particular simulation technique works, e.g. how a simulation-based ligand-docking technique converges on docked solutions. DSMM consequently contains movies of 'molecular motions' that are all 'simulated' but that may illustrate quite diverse aspects of molecular dynamics. There are currently over 100 movies collected in DSMM. Authors are encouraged to enter their own movies into DSMM via the movie submission webpage.

Acknowledgements

Financial support by the Klaus Tschira Foundation is gratefully acknowledged.

References

Giacomo Finocchiaro, Ting Wang, Rene Hoffmann, Aitor Gonzalez and Rebecca C. Wade,
'DSMM - a Database of Simulated Molecular Motions', Nuclear Acids Research, (2003) accepted in the Database issue

Subcategory: Protein structure

Go to the abstract in the NAR 2003 Database Issue.
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