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This Node Is Deprecated — This node is kept for backwards-compatibility, but the usage in new workflows is no longer recommended. The documentation below might contain more information.
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
$SCHRODINGER/utilities/prepwizardOptions
Popular Predecessors
- PDB Reader7 %
- Get PDB5 %
- Row Splitter5 %
- Try (Data Ports)4 %
- Row Filter (Labs)4 %
- Molecule-to-MAE3 %
- File Reader3 %
- Molecule Reader (to MAE)3 %
Protein Preparation Wizard3 %- Row Filter3 %
- Prime Build Homology Model3 %
- MAE-to-Smiles3 %
- Structure Filter3 %
- Parallel Chunk Start3 %
- Glide Grid Generation3 %
- LigPrep2 %
- Prime Minimization2 %
- GroupBy2 %
- SDF Reader2 %
- Assign Bond Orders2 %
- Hierarchical Clustering2 %
- Breakpoint2 %
Table Row To Variable Loop Start2 %- Align Binding Sites2 %
- PDB Downloader (Source)2 %
Loop End2 %- Split by Structure1 %
- Chunk Loop Start1 %
- Add Hydrogens1 %
- Extract Properties1 %
- Prime Side Chain Sampling1 %
- Protein Assignment1 %
- Benchmark Start1 %
- Multiple PdbImporter1 %
- Alignment Reader1 %
- Sequence Reader1 %
- RDKit Interactive Table1 %
- Protein Structure Alignment< 1 %
- PDB Downloader< 1 %
- Partitioning< 1 %
- Delete Atoms< 1 %
- Embrace Minimization< 1 %
- Glide Grid Reader< 1 %
- Glide Sort Results< 1 %
- Induced Fit Docking< 1 %
- MAE-to-Mol2< 1 %
- MAE-to-Pdb< 1 %
- Python Script 1:1< 1 %
- String-to-Type< 1 %
- Load Local PDB Files< 1 %
- PDB Loader< 1 %
- PDB Saver< 1 %
- MolConverter< 1 %
- Java Snippet< 1 %
- Column Filter< 1 %
Joiner< 1 %- RowID< 1 %
- Rule-based Row Splitter< 1 %
CASE Switch Data (Start)< 1 %- String Input (legacy)< 1 %
Read PDB< 1 %- Glide Merge< 1 %
- Residue Scanning< 1 %
- PDB Sequence Extractor< 1 %
- PDB Property Extractor< 1 %
- Advanced MolConverter< 1 %
- Column Splitter< 1 %
- Molecule Type Cast< 1 %
- Container Input (Row)< 1 %
- RDKit From Molecule< 1 %
Views
- Log output
- Log output
Workflows
Binding site 1KNIME Hub- Binding site 1-2KNIME Hub
- Binding site 1-3KNIME Hub
- Binding site shape clusteringKNIME Hub
- Binding site shape clusteringKNIME Hub
- Show all 71 workflows
Links
- No links available
Developers
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