Database
The central part of the MAD ecosystem is a database molecular compounds available for coarse grain
molecular dynamics with the (MARTINI)[1,2,3] force field.
The molecules available in the MAD:Database cover a variety of biochemical
natures across different versions of the MARTINI force field. The database curation process emphasis the qualitative
descriptions of the force field version and parameters used during the coarse graining process that
generated the molecules.
In this tutorial you will learn about:
1. Accessing the database
2. Searching the database for molecules
3. Interactions in search results
4. The content of the molecule card
5. Contributing to the database
beenhere
No registration is required to access, search or download content from the MAD:Database
Access the databases
By default, the database can be consulted by anyone.
The access is located on the left-hand side panel of your browser window.
launch
Just click on the Explore link
Search the database for molecules
The top side of the database welcome screen is dedicated to search parameters.Select-like search criteria
- Force field Search for molecules with at least one coarse grain representation matching selected force field
- Creation way: Search for molecules with at least one coarse grain representation generated by the selected tool/procedure
- Categories: Search for molecule within the selected biochemical category
Free text search criteria
- Name Search for molecules with matching name field.
- History: Search for molecules with matching alias field.
- Upload: Search for molecules with matching author description.
launch
Enter DPG in the Alias search field
Interactions in search results
As you are completing the search section, the table of molecule in the lower-half of the screen is refreshing to display the rows of molecules matching you search.
launch
Click on the molecule named "DPG3"
The content of the molecule card
By default the HEAD version of a molecule is displayed.
Most of the time, this corresponds to the latest deposited coarse grained representation of the molecule.
The visualization screen of the molecular entry is divided into two parts.
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The top level part displays the name and alias of the molecule along with the comments section
of the molecule itp file.
An interactive viewer featuring the same color code as the MAD:Molecule Builder
allows for the visual inspection of the composition and configuration of the molecule.
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The lower part of the screen mentions publication details,
the version tree and gives access to the download section.
info_outline
You can navigate in the version tree and access to all molecular card of its elements.
Each element is a version of the same molecule with alternative an set of parameters or another
force-field version.
You can visit all our in store versions until you find the one matching you needs.
Contributing to the database
file_upload
You don't find your favorite molecule? Add it to the database! Contributions are welcome, we just ask you
to register and you will be able to curate and upload the molecule of your choice.
Your submission will be validated by our moderators prior to its addition to the database.
References
-
SJ Marrink, HJ Risselada, S Yefimov, DP Tieleman, AH De Vries. The MARTINI force field: coarse grained model
for biomolecular simulations. J Phys Chem B (2007) 111, 7812-7824. Doi: 10.1021/jp071097f
-
L Monticelli, SK Kandasamy, X Periole, RG Larson, DP Tieleman, SJ Marrink. The MARTINI coarse-grained force
field: extension to proteins. J Chem Theory Comput (2008) 4, 819-834. Doi: 10.1021/ct700324x
-
Souza, P.C.T., Alessandri, R., Barnoud, J. et al. Martini 3: a general-purpose force field for
coarse-grained molecular dynamics. Nat Methods (2021) 18, 382–388. Doi : 10.1038/s41592-021-01098-3
keyboard_arrow_right The lower part of the screen mentions publication details, the version tree and gives access to the download section.
info_outline
You can navigate in the version tree and access to all molecular card of its elements.
Each element is a version of the same molecule with alternative an set of parameters or another
force-field version.
You can visit all our in store versions until you find the one matching you needs.
Contributing to the database
file_upload
You don't find your favorite molecule? Add it to the database! Contributions are welcome, we just ask you
to register and you will be able to curate and upload the molecule of your choice.
Your submission will be validated by our moderators prior to its addition to the database.
References
- SJ Marrink, HJ Risselada, S Yefimov, DP Tieleman, AH De Vries. The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B (2007) 111, 7812-7824. Doi: 10.1021/jp071097f
- L Monticelli, SK Kandasamy, X Periole, RG Larson, DP Tieleman, SJ Marrink. The MARTINI coarse-grained force field: extension to proteins. J Chem Theory Comput (2008) 4, 819-834. Doi: 10.1021/ct700324x
- Souza, P.C.T., Alessandri, R., Barnoud, J. et al. Martini 3: a general-purpose force field for coarse-grained molecular dynamics. Nat Methods (2021) 18, 382–388. Doi : 10.1038/s41592-021-01098-3