Forge Build Activity Atlas

Options

Basic

Training Set Structure column

The column that contains the aligned molecules to be used as the training set.

Activity column

The name of the column which specifies the activity data to use when building the model.

Units for the input activity values log-transformations

Specify whether the input activity values require log-transforming and give their units.

Similarity column

The name of the column which specifies the similarity data to use when building the model. The values of this column denote how trustworthy the molecule alignment is where 1.0 denotes the molecule alignment is trustworthy while 0.0 denotes the alignment is untrustworthy. If blank then the contents of the 'Similarity_cresset' will be used if available. Otherwise all molecule alignments will be treated as equally trustworthy.

Assign formal charges to input molecules

If set, the protonation states for the input molecules will be set using Cresset's charging rules. Acids will be deprotonated, primary amines protonated, etc.

Activity Atlas

Algorithm

The Activity Atlas algorithm to use. The choice is between the Weighted Sum algorithm, less susceptible to outliers, and the Sum algorithm, the original implementation of the Activity Atlas algorithm.

Grid Spacing

The grid size to use for the analysis. A smaller grid gives finer details, but at the expense of longer calculation time.

Automatically calculate the disparity range

Automatically calculate the disparity range based on the input molecules

Minimum disparity/Maximum disparity

Molecule pairs whose disparity is less than the minimum value will be excluded from the analysis. Pairs whose disparity is greater than the maximum will be treated as though they had the maximum value.
For example, if the range is 5.0-20.0, then pairs with a disparity less than 5.0 are ignored, and those with a disparity of greater than 20.0 treated as though the disparity value was 20.0.

Automatically calculate the activity range

Automatically calculate the activity range based on the input molecules

Inactive if activity below/Fully active if activity above

Molecules whose activity is less than the minimum value will be treated as 'inactive'. Those with more than the maximum value are 'fully active'.
For example, if the range is 6.0-8.0, then any molecule with an activity of less than 6.0 is inactive, any molecule with an activity of more than 8.0 is fully active, and any molecule in between is partially active.

Automatically calculate the similarity range

Automatically calculate the similarity range based on the input molecules

Alignments not trusted if similarity below/Alignments fully trusted if similarity above

Set the similarity thresholds to use when deciding whether a molecule is correctly aligned. Alignments whose similarity value is less than the lower threshold are not trusted at all and are excluded from the calculation. Those with similarity values above the upper threshold are completely trusted and are assumed to be correct. The ones in between are partially trusted.
For example, if the range is 0.6-0.8, then any alignment with a similarity score less than 0.6 will be excluded. Alignments with a similarity of 0.8 or higher are assumed to be correct. An alignment with a similarity score of 0.7 (half way between the thresholds) is assumed to have a 50% chance of being correct.

Molecules required to fully explore a region

Defines the number of molecules whose fields must be seen in a 3D region of space before that region is considered fully explored.

Shape weight

The relative weight assigned to shape (as opposed to field) similarity. Values must be between 0.0 (all field) and 1.0 (all shape).

Optimize pairwise alignments

If checked, the relative orientation of each pair of conformers is optimized by means of a simplex optimizer which rigidly rotates and translates one conformer with respect to maximize the similarity score. Otherwise, the similarity value is computed from fixed input orientations. Turning this option on reduces alignment noise, at the expense of computational cost/time.

Output

Forge project format

Specifies the output format of the Forge project.

• Model only - Creates a Forge project which only contains the model. This option creates a smaller project.
• Molecules and model - Creates a complete Forge project which includes all the molecules and the model.

Write surfaces to Directory

Check this to write the surfaces to a directory.

Output format

Choose the output format for the surfaces:

• Cube
• CCP4
• Insight
• Moe

Selected Directory

Select the output directory for the surfaces.

Overwrite Directory

Check this to overwrite the directory if already present.

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Workflows

• Create an Activity Atlas model using Forge BuildCresset

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