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This Node Is Deprecated — This version of the node has been replaced with a new and improved version. The old version is kept for backwards-compatibility, but for all new workflows we suggest to use the version linked below.
Go to Suggested ReplacementGlide Ligand Docking
Ligand Docking uses Glide to dock ligands into existing grids. The docking calculations
can be carried out in either Standard Precision (SP), Extra Precision (XP), or High-throughput Virtual
Screening (HTVS) mode.
Note1:
If the option to write XP descriptor information is selected, the file 'XPDES_jobID.xpdes' will be saved
in the temporary directory.
Note2:
Always use ungrouped Ligands as input if "Input plus Output" or "Output replaces Input" is selected, so that
the output is matched with the input properly.
Backend implementation
$SCHRODINGER/run glide_sif.py and $SCHRODINGER/glideglide_sif.py is used to write the input file. The command line tool glide is used to implement this node.
Constraints
Currently this node supports "h-bond" and "positional" constraints, which can be selected under the "Constraints" tab. Positional constraints must include a "custom" feature type specifying the SMARTS patterns and the list of atoms that must satisfy the constraint. This can be provided by selecting the feature details cell for the constraint in question. An additional window will open, where the user can either select a text file containing the smarts patterns and atom numbers or manually enter them in a text area. Each smarts pattern should be entered on separate lines using "<SMARTS PATTERN> <ATOM1,ATOM2..>", for example:[N;X2]=C[N;X3] 1
[O;X1]~[N;X3]~[O;X1] 1,3
Multiple atoms can be specified for each pattern, but only one of the specified atoms is constrained. Normally, only one atom should be specified, to ensure that the correct atom is constrained. However, if the functional group contains multiple acceptors or donors, for example, you can specify all of them if you want any one of them to be constrained. This is not necessary for groups such as carboxylates, where the local symmetry of the functional group is used and either of the oxygen atoms in the carboxylate can be selected for the constraint, even though only one of them is specified.
Options
Popular Predecessors
- LigPrep9 %
- Row Filter7 %
- Chunk Loop Start6 %
- Glide Grid Reader5 %
- Glide Grid Generation5 %
Table Row To Variable Loop Start4 %- Rule-based Row Filter4 %
- Phase Screening3 %
- Java Snippet3 %
- SDF Reader3 %
Glide Ensemble Docking3 %Tautomerizer3 %- Chemistry External Tool3 %
- Try (Data Ports)3 %
- Group Loop Start2 %
- RowID2 %
- Row Sampling2 %
- Mol2 Reader2 %
- Epik Classic2 %
- MAE-to-SD2 %
- Molecule Writer (from MAE)2 %
- Molecule-to-MAE2 %
Protein Preparation Wizard2 %- Ungroup MAE2 %
- Table Row to Variable2 %
- Molecule Reader (to MAE)< 1 %
Table Column to Variable< 1 %- Column Filter< 1 %
- Row Splitter< 1 %
Column Rename< 1 %- Java Edit Variable (simple)< 1 %
- ConfGen< 1 %
Ionizer< 1 %- Extract Properties< 1 %
- PDB Reader< 1 %
- Property Filter (Propfilter)< 1 %
- QikProp< 1 %
- Smiles Reader< 1 %
- Bi Reactor< 1 %
- Parallel Chunk Start< 1 %
- Reference Row Filter< 1 %
Views
- Score output of Ligand Docking
- Score output of Ligand Docking
- Log output of Ligand Docking
- Glide Log File
- Report output of GLIDE Ligand Docking
- Report output of GLIDE Ligand Docking
Workflows
Links
- No links available
Developers
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