1. Target definition
All tools in the ProteinsPlus server work on a structure of a protein or a nucleic acid.
In the first step, you need to define this structure either by selecting a structure form the
Protein Data Bank (PDB) via its PDB code (e.g. 2ozr) or upload any other structure in PDB format.
Additional ligand molecules can be provided in SDF format.
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2. Tool selection
Afterwards you can select the tool you are interested in. You can choose SIENA either by selecting it
from the drop-down menu or by following the link under the respective tool description.
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3. Trigger calculation
SIENA searches alternative instances of a given binding site. The query binding site can be defined
by selecting a certain ligand by clicking on the ligands structure diagram or typing its unique identifier
(e.g. GG1_H_2008) into the ligand field. Afterwards, you can trigger a SIENA run with default setting by
just pressing the “Calculate” button. For further information on additional settings, see the mouseover
info buttons next to each setting.
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4. Result
A SIENA calculation results in a list of structures that contain the queried binding site and additional
information on alignment characteristics listed in a result table. Each row represent a certain
structure superimposed with the queried binding site. A structure can be visualized in the NGL viewer
by clicking the red cross in the structure selection area. Click the “-” sign to hide the pocket again.
All structures, the contained ligand molecules, and the binding site alignment can be additionally
downloaded via the download button.
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Publication
For additional information on SIENA, please refer to the corresponding publication:
Bietz, S.; Rarey, M. (2016). SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles.
J. Chem. Inf. Model., 56(1):248-59.
Bietz, S.; Rarey, M. (2015). ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations.
Journal of Chemical Information and Modeling, 55(8):1747–1756.