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 Protoss 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
For running Protoss, no configuration is necessary. Just press the calculation button.
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4. Result
When the calculation is finished, you can visualize the calculated hydrogens using
the “Display hydrogens” button and inspect the structure using the NGL viewer. The whole protonated structure
can be downloaded in PDB format. Additionally, an SD-file containing ligand molecules is provided.
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Publication
For additional information on Protoss, please refer to the corresponding publication:
Bietz, S.; Urbaczek, S.; Schulz, B.; Rarey, M. (2014). Protoss: a Holistic Approach to Predict Tautomers and Protonation States in Protein-ligand Complexes. J Cheminf., 6(12):1-12.