Pharmacophore Screening (Database)

Launches a job that searches a Phase database for matches to a pharmacophore hypothesis. This node iterates through all combinations of hypothesis files, minimum sites to match, and intersite distance matching tolerance.
Note: The job can only be run remotely if the remote host has access to the Phase database - please use the "Remote database" option in that case.

Backend implementation

Options

Column containing hypothesis input

Select column in the data input table containing the hypotheses

Include Log in Output

If selected, a log column will be added to the output table

Database name

The database to be queried

Remote database

Select this option to use a database on a file system that is not accessible to the local host. The full path to the database on the remote file system must be entered into the File name text box. Checking of the database is not done until the job starts.

Source of conformations

Specify whether to use existing conformations or to generate them during the search.

Refine matches

Generate extra conformers for the top-ranked match from each molecule matched. These conformers are subjected to the hit filters and are returned in the hit file. This procedure improves the fitness score, and can return matches when excluded volumes eliminate every match for some molecules.

Use saved matches

Retrieve the existing matches from the database using the match file specified and applies the hit treatment to them

Find new matches

Run the search on the database, retrieve the matches, and apply the hit treatment.

Limit CPU time for matching to N seconds/molecule

Select this option and enter a time in the text box to restrict the amount of CPU time used per molecule in the search. Limiting the CPU time is useful when doing partial matching for hypotheses with many sites, as the time spent finding matches to a given molecule may become very large because of combinatorial considerations.

Save all matches to disk

When deselected, matches are not saved to disk, and you cannot reuse the matches for another search, with different filtering criteria for example. You might want to deselect this option if you expect a large number of hits.

Distance matching tolerance

A list of values is specified. This node iterates through all combinations of hypothesis files, minimum sites to match, and intersite distance matching tolerance.

Minimum number of hypothesis sites to match

A list of values is specified. This node iterates through all combinations of hypothesis files, minimum sites to match, and intersite distance matching tolerance. If "Prefer partial matches involving more sites" is checked, then only the first number of hypothesis sites to match is used, all the rested are grayed out and not used. Not used if the searching method is fetch.

Prefer partial matches involving more sites

If this option is selected, matches involving fewer than n sites will not be sought if there are any matches with n sites

Consider atom types when computing volume scores

Option for computing volume scores using overlap only between atoms of the same MacroModel atom type. This option favors alignments that superimpose chemically similar atoms.

Apply feature-matching rules

Flag for applying feature-matching rules, which associate permitted and prohibited features with each site in the hypothesis. The default is true if hypoID.rules exists and false if not. Note that if the feature rules permit any site to be matched to more than one type of feature, vector scoring will be turned off.

Apply feature-based matching tolerances

Flag for applying feature-specific matching tolerances. The default is true if hypoID.tol exists and false if not.

Apply hypothesis-specific matching tolerances

Flag for applying hypothesis-specific matching tolerances. The default is true if hypoID.dxyz exists and false if not.

Apply site mask to partial matches

Flag for applying a site mask to partial matches. The default is true if hypoID.mask exists and false if not.

Use QSAR model

Flag for applying a QSAR model to hits. The default is true if hypoID.qsar exists and false if not.

Apply excluded volumes

Flag for applying excluded volumes to hits. The default is true if hypoID.xvol or hypoID.ev exists and false if not. If both files exist, hypoID.ev is used.

Return at most

Limit the number of hits listed per molecule - some molecules can return more than one hit because different alignments or different conformers might match the hypothesis.

Fitness score weights

Specify the weights of the alignment score, the vector score and the volume score, and set the threshold for distance matching.

Reject hits with

These three options allow you to reject hits that do not meet the specified cutoff for the given scores. The alignment score cutoff cannot be edited; the other two score cutoffs (vector and volume) can be changed

Views

Std out/err of Find Matches in Phase Screening (Database)

Std out/err of Find Matches in Phase Screening (Database)

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