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 the PPI Server
either by selecting it from the drop-down menu or by following the link under the respective tool description.
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3. Start Calculation
Just press the "Calculate" button for running PPI with default settings. For further
information on additional settings, see the mouseover info buttons next to each setting.
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4. Results
A PPI run results in a probability approximation for each interaction type
(permanent, transient, and artificial contact). Additionally, the interface chains can be depicted in the NGL
viewer by clicking the “Display interface” check box.
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