Step II: Sequence Alignment between target and template protein sequence- target protein sequence is aligned against the template protein sequence using pairwise or multiple sequence alignment (in case if more than one template proteins). A sequence identity of more than 70% between template and target protein allows structure prediction accurately. A sequence identity less than 30% makes structure prediction and modeling of target protein difficult.

Step III: Model building- Template co-ordinates and the alignment information is used to generate a 3-D structure model of the target protein. Fragment analysis and segment analysis are two methods been used to generate the model building. The loop modeling approach is used to model low identity amino stretch in the target protein.

Step IV: Energy minimization- The modeled structure is energy-minimized to obtain the most stable 3-D conformation of the protein.

Step V: Structure validation- The 3-D model of the protein is validated by Ramchandran Plot, Procheck,Verify-3D, Errat Plot. Struture validation can be performed by the structure analysis and validation (SAVS) server http://nihserver.mbi.ucla.edu/.