What dock Can Do for You

The new version of dock can be used in many ways to aid in computational tasks. The following table, Table 1 lists how the new features can be combined together to accomplish different tasks. Only the basic tasks will be discussed in the Getting Started section. Please refer to the Advanced Techniques section (or follow the links contained with the table) for a discussion of each feature and refer to the Reference Manual for a listing of all associated parameters.

 

Table 1. Dock Functionality

flexible_ligand

orient_ligand

score_ligand

multiple_ligands

chemical_screen

parallel_jobs

Perform a Conformation Search of a molecule.

X

 

 

 

 

 

Generate configurations of a molecule in a site.

X

X

 

 

 

 

Dock a flexible molecule (with Anchor-First Search optional).

X

X

X

 

 

 

Dock a database of flexible molecules.

X

X

X

X

 

 

Generate conformations and compute internal scores.

X

 

X

 

 

 

Generate conformations for a database of molecules.

X

 

 

X

 

 

Key a database for a Chemical Screen (similarity or pharmacophore).

X

 

 

X

X

 

Parse a database, processing each conformer by Parallel Jobs .

X

 

 

X

 

X

Perform an Orientation Search of a molecule in a site.

 

X

 

 

 

 

Perform rigid docking of the input conformation of a molecule.

 

X

X

 

 

 

Perform rigid docking of a database.

 

X

X

X

 

 

Perform Scoring or Score Optimization of input position of a molecule.

 

 

X

 

 

 

Score/minimize database of molecules or molecule configurations.

 

 

X

X

 

 

Read/write a database of molecules (file format conversion).

 

 

 

X

 

 

Filter a database by Chemical Screen (similarity or pharmacophore).

 

 

 

X

X

 

Parse a database, processing each molecule by Parallel Jobs .

 

 

 

X

 

X

 

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