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Answer Posted / anubrata das
if the crystal structure of any protein is unavailable,
then one can use the tools of homology modelling to
determine the structure. the logic is that a similar
structure arises becuse of a similar sequence of amino
acids. for homology modelling to be accurate an identity
match of 70% is desirable.basically, one does a FASTA
search of A.A sequences in the PDB database (A.A sequences
whose structures are known), does a CLUSTAL alignment to
check for conserved residues. then the structure of the
unknown A.A sequence is built up on the basis of the
structure of the best matches in FASTA and CLUSTAL by
programs like LLOOP and HHPRED. this structure can be
visualized in programs like DEEPVIEW,Protein Explorer
etc.the EXPASY proteomics server is a good site to begin
with - http://swissmodel.expasy.org/
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