Nucleic Acids Research, 2003, Vol. 31, No. 1 456-457
© 2003 Oxford University Press
DSMM: a Database of Simulated Molecular Motions
1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany 2 European Media Laboratory, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany
*To whom correspondence should be addressed Fax: +49 6221533298; Email: rebecca.wade{at}eml.villa-bosch.de
Received August 14, 2002; Revised and Accepted September 23, 2002
ABSTRACT
We describe a Database of Simulated Molecular Motions (DSMM). 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/mcm/database/dsmm.
INTRODUCTION
Molecules are far from static. In biological systems, they are constantly in a state of motion, both moving around and undergoing fluctuations and transitions in their conformations. Dynamic motions are crucial to the function of biological molecules (1). Enzymes, for example, can become inactive when cooled below ca. 220K, the temperature below which anharmonic motions are absent (2).
Many molecular modeling and simulation studies have contributed to our understanding of biomolecular dynamics (3). 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 an 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, the Database of Simulated Molecular Motions (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. DSMM is complementary to the Database of Macromolecular Movement (4) (http://molmovdb.mbb.yale.edu/MolMovDB) which contains animations created by morphing between experimentally determined structures of molecules in different conformations. DSMM can be considered a step towards a more complete database containing trajectories from molecular dynamics simulations and the data necessary to generate and analyze them.
DESCRIPTION
The DSMM database was built using the relational database management system MySQL. It has been made accessible for querying via a webserver by using the server-side scripting language PHP. Both MySQL and PHP are freely downloadable software. There are currently over 100 movies collected in DSMM. These cover a wide spectrum of molecular dynamics including the dynamics of biomolecular conformations, molecular diffusion, protein-ligand docking, reaction product release, substrate access channels, ion channels, water channels and catalytic reactions. Each movie is characterized by the following fields: identifier (ID), molecular function, molecular structure, author, author's institution, author's email address, reference, description, method, file type and size and a hyperlink to the web page from which the movie can be downloaded. All movies can be browsed and listed by movie ID, molecular name or method. A specific movie can be found by searching the method, the type of molecule, the function, the biomolecule, the file type, the molecular structure and/or the author. Figure 1 shows a screenshot illustrating usage of DSMM. Authors are encouraged to enter their own movies into DSMM via the movie submission webpage.
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ACKNOWLEDGEMENTS
Financial support by the Klaus Tschira Foundation and helpful discussions with Isabel Rojas and Razif Gabdoulline (EML) and Aidan Budd (EMBL) are gratefully acknowledged.
REFERENCES
- Eisenmesser,E.Z., Bosco,D.A., Akke,M. and Kern,D. (2002) Enzyme dynamics during catalysis. Science, 295, 1520–1523.
[Abstract/Free Full Text] - Rasmussen,B.F., Stock,A.M., Ringe,D. and Petsko,G.A. (1992) Crystalline ribonuclease loses function below the dynamical transition at 220K. Nature, 357, 423–424.[CrossRef][Medline]
- Karplus,M. (2002) Molecular dynamics simulations of biomolecules. Acc. Chem. Res., 35, 321–323 and other articles in this issue of Acc. Chem. Res.[CrossRef][Web of Science][Medline]
- Gerstein,M. and Krebs,W.G. (1998) A database of macromolecular motions. Nucleic Acid. Res., 26, 4280–4290.
[Abstract/Free Full Text]
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