IGLA-3D is a modular method for construction of pairwise 3D alignments (superpositions) of protein structures. It consists of the high-level control module and four special-purpose modules:
the first module (IS) constructs an initial superposition of two protein structures or an initial core, the second module (AC) constructs alignment core given proteins superposition, the third module (FM) finds a motion (shift and rotation) that optimally superimposes the alignment core, the forth module (SM) evaluates the similarity of proteins given a 3D alignment of these proteins.
The control module unites the special-purpose modules using one of the standard schemes for iterative 3D alignment algorithms (the scheme choice depends on the type of the IS module):
The benefit of modularity is the fact that a module can be easily replaced by another module that solves the same task. Hence, if different modules are implemented for one task, one can easily find the best combination for his purposes. For example, testing showed that for certain tasks SM modules that use biological information along with standard geometrical information significantly increase the quality of results in comparison with SM modules that use only geometrical information.
The currents version of IGLA-3D web-service uses the fixed special-purpose modules:
However, in future versions of the IGLA-3D web service the users will be able to select the special-purpose modules to be used by the control module from a given list - one module for each task
 Y. Zhang, J. Skolnick (2005), TM-align: a protein structure alignment algorithm based on the TM-score // Nucleic Acids Research, 33(7): 2302-2309.
 W. Kabsch (1978), A discussion of the solution for the best rotation to relate two sets of vectors // Acta Crystallogr. A, 34: 827-828.
 L. Holm, C. Sander (1993), Protein Structure Comparison by Alignment of Distance Matrices // J. Mol. Biol., 233: 123-138.