At sequence alignment we do not get complete similarity for all the sequences. There will be similar regions as well as variable regions. The similar regions are structurally conserved regions (SCRs) where as the variable regions are variable regions (VRs).When we align known structures, they are examined to identify the structurally conserved regions (SCRs) from which an average structure, or framework, can be made for such regions of the proteins. We have to identify even the variable regions because some technique may be applied to model these regions of unknown proteins. If we have only one known structure it becomes more difficult to find SCRs.In this situation we have to go with the analysis of other homologues for which multiple sequences are available, since the SCRs generally correspond to the secondary structural elements such as alpha-helices and beta-sheets, and to the ligand- and substrate-binding sites. Therefore, such regions are employed as the SCRs in the cases where only one structure is accessible. The VRs generally lie on the surface of the proteins and form the loops where the main chain turns. After the completion of alignment of known sequences, we go with the alignment of unknown sequences. Here we can use the alignment that is based solely on sequence. Though the other structural features may also be taken into account. There are multiple sequence algorithms available in quanta which can be used in the alignment of both known structures as well as in the alignment of unknown with the known structures. There are scoring systems that can be evaluated during an alignment so that relative statistical weights may be assigned.
The four scoring techniques are as:
• Sequence homology which has the conventional scoring system Needleman-Wunsch alignment.
• Secondary structure homology in which scoring is based on the probability of replacing one secondary structure type by other type. Secondary structural features are based on hydrogen-bonding patterns and main chain torsions, by the definitions of secondary structure types being those of Kabsch and Sander. When applying this method with the unknown, its secondary structure should be predicted first using one of the three (Momany, GOR, and Holley/Karplus) methods available in Quanta
• Residue accessibility homology is reliant on the difference in the fractional accessibility between aligned residues
• CA-CA distance homology that is based on the interatomic distances between the alpha carbon atoms of the aligned residues.