Future Works

Our peptide modeling method is based on genetic algorithm and bmPDA block assembly method. The performance is good locally but not so good in large molecules. Application on the structure prediction of epitopes is perfect, because they are consisted of about 8-12 amino acids. But if we want apply our method on structure prediction of large proteins, the impact of protein folding still need to be considered.

Despite the good accuracy of our QSAR-SVR epitope prediction method, the time-consuming peptide modeling process was the rate-determine step in our method. The block picking process during genetic algorithm may be speedup by block clustering.

Docking is a time-consuming process. Compare to other docking software, the Molegro Virtual Docker is more accurate and fast. However, if there is a faster and accurate docking software, the process can still be speed-up.

There are several directions for future research:

1. More peptide Segment sizes: Our epitope modeling method is limited to predict 9mers peptides till now. It can be applied to prediction on arbitrary length of protein. However, accuracy is still our concern.

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2. Structure clustering on FluV neutralization epitopes and predictive immune evasions on FluV neutralization epitope

3. Extend the viral oncogenesis model of HLA1 immune evasion at agretope on miscellaneous viruses such as HBeAg

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Appendix A

List of Publications

Journal Papers:

范振杰;林堂烈 (2003): “以懸壅垂顎皮瓣治療打鼾 Uvulopalatal Flap for Snoring” 臺灣耳 鼻喉頭頸外科雜誌 38(2): 56~60 (2003, 03-04).

Hsueh-Ting Chu, William W. L. Hsiao, Chen-Chieh Fan, Chaur-Chin Chen and Cheng-Yan Kao (2012): “SeqEntropy: quantitative evaluation of sequence repeats for short read genome sequencing” (submitted)

Conference Papers:

Yu-Ju Chuang, Hsueh-Ting Chu, Chen-Chieh Fan and Kao Cheng-Yan (2009): “Prediction For Multi-epitope HCA661 Liver Cancer Vaccines”. Asia Pacific Bioinformatics Conference 2009.

Chen-Chieh Fan, Chun-Fan Chang, Hsueh-Ting Chu, and Cheng-Yan Kao (2012):

“Implement Web-version Bio-mimicry Peptide Design Algorithm from Trimer Alpha-carbon Mining towards Tri-peptide Fusing”. Symposium on Cloud and Services Computing 2012.

Chun-Fan Chang, Chen-Chieh Fan, and Cheng-Yan Kao (2012): “Improve NPC CMI Likely on HLA-Agretope Docking in EBV-LMP1 Antigen of Putative Nona-peptide Structure from Peptide Design Algorithm Based on Tri-alpha-carbon Mining towards Tri-peptide Fusing”.

11th International Conference in Bioinformatics (submitted)

Hsueh-Ting Chu, William W. L. Hsiao, Theresa T. H. Tsao, Ching-Mao Chang, Yen-Wenn Liu, Chen-Chieh Fan, Han Lin, Hen-Hong Chang, Tze-Jung Yeh, Jen-Chih Chen, Chaur-Chin Chen and Cheng-Yan Kao (2012): “Quantitative assessment of mitochondrial DNA copies from whole genome sequencing as a biomarker of aging” 11th International Conference in Bioinformatics (submitted)

Chun-Fan Chang, Chen-Chieh Fan and Cheng-Yan Kao (2012): “Improving CMI Likely from Docking HLA-1 Pit and Putative Agretope towards Mining Anchor- modified DNA Vaccine for in vitro Cell Activation and Action Complex Enhancement Drugs for in vivo Subject Therapy”. Translational Bioinformatics Conference 2012 (submitted)

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Patent Applications:

USA provisional patent:

Chun-Fan Chang, Cheng-Yan Kao, Thai-Yen Ling, Chen-hsiung Chan, Sheng-An Lee, Yu-Lun Kuo, Chen-chieh Fan, Fan-Chiang Sung (2009): CMI-inhibitory and/or CMI-stimulatory Modulators on AMI-naive and/or AMI-miscellaneous Status (Application No. 61/180,127; Filing Date: May 20, 2009)

USA utility patent:

Chun-Fan Chang, Wen-Chieh Chang, Tsung-Jui Chen, Chen-Chieh Fan, and Cheng-Yan Kao (2012): Method of restoring composite counter-balancing waveform compartments and extracting decomposite action waves from a composite waveform measurement and/or compartment derivatives of a corresponding operation system. (Application No. 13/526,525;

Filing Date: June 18, 2012)

Taiwan

高成炎;高成榮;范振杰;朱學亭;張春梵。2010。睡眠呼吸中止防護裝置。中華民國發明 專利第 M392409 號