Prediction of DNA-binding protein based on alpha shape modeling

Weiqiang Zhou, Hong Yan

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Previous studies about protein-DNA interaction focused on the bound structure of DNA-binding proteins and provided good but not practical results. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and use structural alignment to develop an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of unbound DNA-binding protein. The proposed method provides good performance in predicting unbound structure of DNA-binding protein which is potentially useful in many fields. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve sensitivity ranges from 48.08% to 44.23% and specificity ranges from 73.82% to 84.29%.

Original languageEnglish (US)
Title of host publicationProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Pages23-28
Number of pages6
DOIs
StatePublished - 2010
Externally publishedYes
Event2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 - Hong Kong, China
Duration: Dec 18 2010Dec 21 2010

Publication series

NameProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010

Other

Other2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Country/TerritoryChina
CityHong Kong
Period12/18/1012/21/10

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

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