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Protein Preparation Wizard

Schrödinger extension for KNIME Workbench version by Schrödinger

The Protein Preparation Wizard allows you to take a protein from its raw state, (which may be missing hydrogen atoms and have incorrect bond order assignments, charge states, or orientations of various groups) to a state in which it is properly prepared for calculations using Schrödinger products such as Glide, Prime, QSite, Liaison, and MacroModel.
Note: Distributed jobs can only be carried out if input is Maestro type, please enter the number of jobs to run on the specified host and number of processors.

Backend implementation



Column containing structures
Column in the input data table containing the protein structures.
Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaces Input - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Assign bond orders
Assign bond orders to het groups.
Add hydrogens
Add hydrogens to the structure.
Treat metals
Break bonds to metals and correct formal charges to metals and neighboring atoms.
Convert Selenomethionine residues to Methionines.
Treat disulfides
Create bonds to proximal Sulfurs (delete hydrogens as needed).
Delete waters
Delete waters #A from het groups (default is 5).
Fill loops
Fill in missing loops from the SEQRES records in the PDB file, using Prime. The input PDB structure can be in either PDB or Maestro format.
Cap termini
Add ACE (N-acetyl)and NMA (N-methyl amide) groups to N and C termini.
Sample water orientations
ProtAssign: sample waters.
Minimize to RMSD
Run Glide protein prep, constrained refinement (Impref) using the RMSD cutoff (default is 0.3).
Hydrogens only
Impref: Fix heavy atoms (minimize hydrogens only).
Number of subjobs
If not selected, total number of processors will be used as subjobs count
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Flow variable prefix keyword: PrepWizard
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option from command line, just specify the option_name and the value as _off_ through the flow variable.

Input Ports

Input molecule Maestro or PDB format

Output Ports

Output molecule in Maestro format


Log output
Log output

Best Friends (Incoming)

Best Friends (Outgoing)



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