Protein surface search in DNA-binding protein prediction by Delaunay triangulation modeling

Po Han Cheng, Hung Yu Chen, Hung-Yu Kao

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

2 Citations (Scopus)

Abstract

Various protein researches have been published, such as transcription factor prediction, DNA-binding protein prediction, homology modeling, and protein-protein interaction. Structure alignment techniques have played an important role in those researches. Many protein alignment methods have been brought up, yet only few have concentrated on protein surfaces. Among this research, we have developed a DNA-binding protein prediction system based on protein surface search, using Voronoi diagram and Delaunay triangulation to model molecular surface. Also, we designed an iterative method to construct a consecutive and closed surface of protein. Finally, a system integrating surface structure information is applied to search common surface of proteins, and to predict protein-DNA interaction. While comparing to our previous method, there's a significant increase of inner triangles identified and removed. Furthermore, experimental data showed that our method has better performance in identifying surface residues than the widely used method using an RASA cutoff. Besides, as we search the entire Protein Data Bank (PDB) for similar surface to Estrogen Receptor α (ERα), we discovered that the majority of the family of ERα in Ppfam has been found with high scores. Finally, we compared our data with results of chemical experiment that suggest several proteins tending to bind to Estrogen Response Elements (ERE), finding an interesting result that the 14-3-3β protein with high score in our prediction is proven to bind to ERE in the further chemical experiment.

Original languageEnglish
Title of host publicationICS 2010 - International Computer Symposium
Pages783-788
Number of pages6
DOIs
Publication statusPublished - 2010 Dec 1
Event2010 International Computer Symposium, ICS 2010 - Tainan, Taiwan
Duration: 2010 Dec 162010 Dec 18

Publication series

NameICS 2010 - International Computer Symposium

Other

Other2010 International Computer Symposium, ICS 2010
CountryTaiwan
CityTainan
Period10-12-1610-12-18

Fingerprint

Triangulation
DNA
Proteins
Carrier Proteins
Transcription factors
Iterative methods
Surface structure
Experiments

All Science Journal Classification (ASJC) codes

  • Computer Science(all)

Cite this

Cheng, P. H., Chen, H. Y., & Kao, H-Y. (2010). Protein surface search in DNA-binding protein prediction by Delaunay triangulation modeling. In ICS 2010 - International Computer Symposium (pp. 783-788). [5685406] (ICS 2010 - International Computer Symposium). https://doi.org/10.1109/COMPSYM.2010.5685406
Cheng, Po Han ; Chen, Hung Yu ; Kao, Hung-Yu. / Protein surface search in DNA-binding protein prediction by Delaunay triangulation modeling. ICS 2010 - International Computer Symposium. 2010. pp. 783-788 (ICS 2010 - International Computer Symposium).
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Cheng, PH, Chen, HY & Kao, H-Y 2010, Protein surface search in DNA-binding protein prediction by Delaunay triangulation modeling. in ICS 2010 - International Computer Symposium., 5685406, ICS 2010 - International Computer Symposium, pp. 783-788, 2010 International Computer Symposium, ICS 2010, Tainan, Taiwan, 10-12-16. https://doi.org/10.1109/COMPSYM.2010.5685406

Protein surface search in DNA-binding protein prediction by Delaunay triangulation modeling. / Cheng, Po Han; Chen, Hung Yu; Kao, Hung-Yu.

ICS 2010 - International Computer Symposium. 2010. p. 783-788 5685406 (ICS 2010 - International Computer Symposium).

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

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Cheng PH, Chen HY, Kao H-Y. Protein surface search in DNA-binding protein prediction by Delaunay triangulation modeling. In ICS 2010 - International Computer Symposium. 2010. p. 783-788. 5685406. (ICS 2010 - International Computer Symposium). https://doi.org/10.1109/COMPSYM.2010.5685406