Genome sequencing projects has produced a vast wealth of data describing the protein coding regions of the genome under study. However, only a minority of the protein sequences identified has a clear sequence homology to a known protein. In such cases valuable three-dimensional models of the protein coding sequence can be constructed by homology modeling methods. Threading methods uses specialized schemes to relate protein sequences to a library of known structures. Even in cases where there is no clear sequence homology, they have been shown to be able to identify the likely protein fold. As collaborative efforts in systematic structure determination begins to develop in the future, the number of protein sequences that cannot be assigned to a structural class by homology or threading methods will decrease, simply because they belong to a previously unidentified protein folding class. Moreover, the differences in substrate specificity may be explained on the basis of the predicted structures of the protein and its complex with the substrate. Natural products have been a rich source in providing leads for the development of drugs for the treatment of different infections. For this reason,in silico modeling methods in conjunction with natural products are likely to become increasingly useful in the near future for structure-based drug design approaches.
Key words: homology modeling, natural products, drug discovery.
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