%0 Journal Article
	%A Yi-Zhong Weng and  Chien-Kang Huang and  Yu-Feng Huang and  Chi-Yuan Yu and  Darby Tien-Hao Chang
	%D 2009
	%J International Journal of Computer and Information Engineering
	%B World Academy of Science, Engineering and Technology
	%I Open Science Index 29, 2009
	%T Introducing Sequence-Order Constraint into Prediction of Protein Binding Sites with Automatically Extracted Templates
	%U https://publications.waset.org/pdf/2272
	%V 29
	%X Search for a tertiary substructure that geometrically
matches the 3D pattern of the binding site of a well-studied protein provides a solution to predict protein functions. In our previous work,
a web server has been built to predict protein-ligand binding sites
based on automatically extracted templates. However, a drawback of such templates is that the web server was prone to resulting in many
false positive matches. In this study, we present a sequence-order constraint to reduce the false positive matches of using automatically
extracted templates to predict protein-ligand binding sites. The binding site predictor comprises i) an automatically constructed template library and ii) a local structure alignment algorithm for
querying the library. The sequence-order constraint is employed to
identify the inconsistency between the local regions of the query protein and the templates. Experimental results reveal that the sequence-order constraint can largely reduce the false positive matches and is effective for template-based binding site prediction.
	%P 1456 - 1462