Explain Homology modeling

Question

Explain brief the term Homology modeling?

Answer 1

When crystal structure of any protein is inaccessible, then one can employ the tools of homology modeling to find out the structure. The logic is which the similar structure arises due to a same sequence of amino acids. For homology modeling to be precise an identity match of seventy percent is desirable. Generally, one does a FASTA search of A.A sequences in PDB database (A.A sequences whose structures are recognized), does a CLUSTAL alignment to check for the conserved residues. Then the structure of unknown A.A sequence is built on the basis of structure of the best matches in the FASTA and CLUSTAL through the programs like LLOOP and HHPRED. This structure can be visualized in the programs like DEEPVIEW, Protein Explorer and so forth.