Homologous proteins often have similar structures. A structure alignment attempts to identify these similarities by comparing the shape and 3D conformation between two structures. Unlike simple superposition methods, structure alignments do not require prior knowledge of equivalent residues between structures.

The results of a structure alignment are viewed in the Structure view as a set of superimposed structures, where each alignment minimizes the root mean squared deviation (RMSD), or the average distance between atoms in superimposed structures. The RMSD values are also reported in the Details panel for a group of structures. Rigid-body alignment is used to determines the best alignment without allowing the structures to bend or twist.

The following video shows a brief walkthrough of the structural alignment workflow:

To align multiple structures:

  1. Open a document containing two or more structures.
  1. (optional) If you wish to align specific regions, select the desired regions. Each selection must contain more than 8 residues with atomic coordinates.
  1. For whole structures, choose between Structure > Align Structures > Rigid-body Alignment (TM-Align) and Structure > Align Structures > Rigid-body Alignment (jFATCAT).

If you have selected specific regions to align, choose between Structure > Align Structures > Rigid-body Alignment for Selected Regions (TM-Align) and Structure > Align Structures > Rigid-body Alignment for Selected Regions (jFATCAT).

Protean 3D will then calculate a series of pairwise structure alignments using the first structure in the document as the alignment base.

If the Structure > Align Structures command is disabled, the usual sub-command is replaced by one of the following:

Sub-command Correction procedure:
No Document Open Follow step 1, above.
Requires Two or More Protein Structures Add one or more structures to the existing structure using File > Add to Document.
Requires Selections in Two or More Protein Structures (Each > 8 Residues) You cannot align multiple regions from the same structure. You need to select regions in two or more structures, as per step 2, above.

References for Protean 3D’s structure alignment algorithms include Prlic et al. (2010), Ye et al. (2003) and Zhang and Skolnick (2005). The last of these pertains specifically to the TM-Align method.

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