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ZBH - Center for Bioinformatics

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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