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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 EDIA 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 EDIA, no configuration is necessary. Just press the calculation button.
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4. Result
EDIA calculates an individual quality score for each atom, which represents how well this
atoms position is supported by the experimental electron density. These scores are encoded in a coloring scheme,
where blue represents a good and red a poor support. All atoms are accordingly colored in the NGL viewer.
“Display electron density” button can be applied for a visual inspection of the electron density at a level of 1σ.
Further information on medium EDIA values for residue and ligand substructures are given in a result table.
All information can be additionally downloaded using the download button.
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Publication
For additional information on EDIA, please refer to the corresponding publications:
Meyder, A.; Nittinger, E.; Lange, G.; Klein, R.; Rarey, M. (2017). Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. J. Chem. Inf. Model., 57 (10), pp 2437–2447.
Nittinger, E.; Schneider, S.; Lange, G.; Rarey, M. (2015). Evidence of Water Molecules—A Statistical Evaluation of Water Molecules Based on Electron Density. J. Chem. Inf. Model., 55 (4), pp 771–783.