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. 1xm6) or upload any other structure in PDB format. Additional ligand molecules can be provided in SDF format. Click on image to jump to that page.
3. Trigger calculation
For running JAMDA a binding site has to be defined, either by selecting a reference ligand or using a pocket. Furthermore, molecules for docking must be selected. Here, either a molecule file can be uploaded or a ligand from the PDB file can be used. All other settings are optional and may be accessed via the 'Advanced options' tab.
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