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.
Click on image to jump to that page.
2. Tool selection
Afterwards you can select the tool you are interested in. You can choose METALizer 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
METALizer predicts the coordination geometry of metals in metalloproteins. The query
binding site can be defined by selecting a metal atom from the list of ligands by clicking on the ligands
structure diagram or typing its unique identifier (e.g. Metalatom: [CA]4040:H.CA) into the ligand field.
Afterwards, you can trigger a METALizer run with default setting by just pressing the “Calculate” button, or
you may choose a specific cutoff. For further information on additional settings, see the mouseover info
buttons next to each setting.
Click on image to jump to that page.
4. Result
METALizer predicts multiple possible geometries for the selected metal atom, based on
its surrounding atoms in the chosen protein. These geometries can individually be visualized by the NGL viewer.
Additionally, statistics of the geometries and distances for the metal ion can be displayed based on the whole
PDB or on an ensemble of structurally similar binding sites generated with SIENA. Another option is the EDIA
filter to detect atoms that are poorly supported by electron density. These are then excluded from the
METALizer analysis.
Click on image to jump to that page.
4. Result (continued)
METALizer predicts multiple possible geometries for the selected metal atom, based on
its surrounding atoms in the chosen protein. These geometries can individually be visualized by the NGL viewer.
Additionally, statistics of the geometries and distances for the metal ion can be displayed based on the whole
PDB or on an ensemble of structurally similar binding sites generated with SIENA. Another option is the EDIA
filter to detect atoms that are poorly supported by electron density. These are then excluded from the
METALizer analysis.
Click on image to jump to that page.
