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Virtual Screening Workflow — Preparation Tab |
This tab allows you to make settings for ligand preparation, which is done with LigPrep. If your ligands are already 3D structures in the appropriate ionization and tautomeric state, you can deselect the Prepare ligands option.
Select this option to prepare the ligands with LigPrep.
Regularize the input geometries, so that ligands that are identical apart from small deviations in the atom positions are always treated the same. This option uses a conversion to unique SMILES to ensure the same atom numbering and geometry.
When regularizing input geometries, remove any duplicates. The next three options apply when duplicates are removed.
Remove small molecules and ions from structures (as in LigPrep) before comparing structures for duplicates.
Neutralize structures (as in LigPrep) before comparing structures for duplicates.
Merge properties from duplicates. If the properties have different values, the property is converted to a string that lists the values.
Generate ionization and tautomeric states that have significant probability in the given pH range. Enter the target pH and the range in the text boxes.
Select the program for generating states. Selecting Ionizer generates ionization states with the
ionizer program, and tautomeric states with the
tautomerizer program, separately. Selecting Epik generates ionization and tautomeric states with Epik at
the same time.
Generate extra states that are suitable for binding to metals in proteins, using Epik. Only available when Epik is selected for state generation.
Select this option to remove ionization and tautomeric states that have high energies. These are states that are likely to have low populations at the prevailing conditions.
These options allow you to specify the source of stereochemical information. If you have 3D structures, select 3D geometry to determine the stereochemistry from the geometry. Otherwise, select Specified 2D stereo properties, to use information from the stereochemical properties in the input file. Any stereochemical center whose chirality is not determined from this information will have its chirality varied.
Enter the maximum number of stereoisomers to be retained by LigPrep in this text box. LigPrep generates up to 32 stereoisomers, which are then filtered to retain those with the lowest energies. Note that the LigPrep run preserves any existing chirality information in the input file, and selects starting chiralities based on the chemistry of naturally occurring steroids, fused rings and peptides.
Enter the maximum number of ring conformations to be generated by LigPrep in this text box.
Sample conformations of 7-membered and larger rings with MacroModel after ligand preparation. These ring conformations are not sampled by LigPrep.
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