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.
2. Tool selection
Afterwards you can select the tool you are interested in. You can choose JAMDA either by selecting it from the drop-down menu or by following the link under the respective tool description. 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.
4. Result
JAMDA predicts protein-ligand poses for the docked molecules. All information can be additionally downloaded using the download button. Click on image to jump to that page.
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