Yi-Zhong Weng and Chien-Kang Huang and Yu-Feng Huang and Chi-Yuan Yu and Darby Tien-Hao Chang
Introducing SequenceOrder Constraint into Prediction of Protein Binding Sites with Automatically Extracted Templates
1456 - 1462
2009
3
5
International Journal of Computer and Information Engineering
https://publications.waset.org/pdf/2272
https://publications.waset.org/vol/29
World Academy of Science, Engineering and Technology
Search for a tertiary substructure that geometrically
matches the 3D pattern of the binding site of a wellstudied protein provides a solution to predict protein functions. In our previous work,
a web server has been built to predict proteinligand 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 sequenceorder constraint to reduce the false positive matches of using automatically
extracted templates to predict proteinligand 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 sequenceorder constraint is employed to
identify the inconsistency between the local regions of the query protein and the templates. Experimental results reveal that the sequenceorder constraint can largely reduce the false positive matches and is effective for templatebased binding site prediction.
Open Science Index 29, 2009