Align Binding Sites Panel

In this panel you can align the binding sites (or other structural features) of members of a family of proteins. The job first runs a global alignment and then automatically generates the list of atoms to use in a pairwise alignment from the residues selected for the alignment.

To open the Align Binding Sites panel: click the Tasks button and browse to Structure Alignment → Binding Site Alignment.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see align_binding_sites Command Help and Structure Alignment: align_binding_sites.

  • Features
  • Additional Resources

Align Binding Sites Panel Features

 

Use proteins from controls

The option menu provides choices of the source of protein structures. The choices are:

  • Project Table—Use the entries that are selected in the Project Table for alignment. The first entry in the Project Table (lowest row index) is used as the reference structure.
  • Workspace—Use the entries that are included in the Workspace for alignment. The first included entry in the Project Table (lowest row index) is used as the reference structure.
  • File—Read the structures from one or more files. The first structure in the first file is used as the reference structure. When you choose File, the Input file text box and Browse button become available, and you can browse for the input files.
Residues for alignment section

In this section you select the residues that are to be used to align the proteins. There are two main options:

Automatically detect binding site residues

Select the binding site residues based on a distance from the ligand. The distance is specified in the Align residues withinNÅ from the ligand text box. Two options are available for specifying the ligand:

  • Detect ligand automatically—Detect the ligand by selecting the molecule that is most ligand-like (number of atoms).
  • Use molecule number—Specify the ligand by molecule number. You can enter a number in the text box, or select Pick ligand and pick a ligand atom in the Workspace.
Manually select residues

This option allows you to specify individual residues. You can define the residues in one of three ways:

  • Enter the residue specification in the Align residues text box, in the format chain:number.

  • Click Select residues to open the Atom Selection Dialog Box and define the residues.

  • Select Pick a residue to include/exclude and pick residues in the Workspace. Picking an already included residue excludes it.

Ignore pairs greater than N Å apart text box

If the atoms in an atom pair are greater than the specified distance apart, do not use this pair in the alignment process. This test applies to the atom pairs defined by the residues selected for alignment.

Structures are prealigned option

Suppress the global alignment of the protein structures, and align only by using the selected residues.

In place (calculate RMSD only) option

Calculate the RMSD between prealigned protein structures, without doing any alignment.

Use optimized settings option

Run a scanning alignment with three window lengths, of 8, 9, and 13 residues, and return the best results. These values have proved to provide good results for a series of cases in which alignment fails, such as multi-chain proteins and proteins with low similarity. Using this option takes longer, because three alignments are run. This option is selected by default.

Reset button

Reset the panel to its default state.

Tutorials

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