This is the first version of the SPACEBALL server.
The parameters are explained in our paper M. Chwastyk, M. Jaskolski and M. Cieplak, Structure-based thermodynamic and mechanical stability of plant PR-10 proteins with cavities, FEBS J. 281: 416-429 (2014) (see
To start the calculations you should provide adequate parameters. Fields marked by an asterisk (*) are entries that are required.
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We recommend not to change any of the default parameters except that the bigger number of rotations, the more accurate the result. However, 100 rotations is very accurate.
You should copy and paste the PDB file of your structure into the correct field. It is important to keep the standard PDB format.
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A probe's radius: Å (*)
Grid in the x direction: Å (*)
Grid in the y direction: Å (*)
Grid in the z direction: Å (*)
Number of rotations: (*)
If the structure file contains nucleotides, should they be taken into account?
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