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 DoGSiteScorer
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 DoGSiteScorer with default settings.
For further information on additional settings, see the mouseover info buttons next to each string.
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4. Results
A DoGSiteScorer calculation results in a list of potential pocket of the given structure and
additional information on pocket characteristics listed in a result table. Each row represents
a certain pocket and its features. A pocket can be visualized in the NGL viewer by clicking the red cross
in the pocket selection area. Click the “-” sign to hide the pocket again. All information can
be additionally downloaded via the download button.
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Publications
For additional information on DoGSiteScorer, please refer to the corresponding publications:
Volkamer, A., Griewel, A., Grombacher, T., Rarey, M. (2010). Analyzing the Topology of Active Sites: On the Prediction of Pockets and Sub-pockets. Journal of Chemical Information and Modeling, 50(11):2041-2052.
Volkamer, A., Kuhn, D., Grombacher, T., Rippmann, F., Rarey, M. (2012). Combining Global and Local Measures for Structure-Based Druggability Predictions. J. Chem. Inf. Model., 52(2):360-372.