iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Jianhua JiaKuo-Chen Chou

Abstract

Knowledge of protein-protein interactions and their binding sites is indispensable for in-depth understanding of the networks in living cells. With the avalanche of protein sequences generated in the postgenomic age, it is critical to develop computational methods for identifying in a timely fashion the protein-protein binding sites (PPBSs) based on the sequence information alone because the information obtained by this way can be used for both biomedical research and drug development. To address such a challenge, we have proposed a new predictor, called iPPBS-Opt, in which we have used: (1) the K-Nearest Neighbors Cleaning (KNNC) and Inserting Hypothetical Training Samples (IHTS) treatments to optimize the training dataset; (2) the ensemble voting approach to select the most relevant features; and (3) the stationary wavelet transform to formulate the statistical samples. Cross-validation tests by targeting the experiment-confirmed results have demonstrated that the new predictor is very promising, implying that the aforementioned practices are indeed very effective. Particularly, the approach of using the wavelets to express protein/peptide sequences might be the key in grasping the problem's essence, fully consistent with the...Continue Reading

References

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Oct 4, 2005·Journal of Theoretical Biology·Hong-Bin ShenKuo-Chen Chou
Feb 7, 2006·Journal of Proteome Research·Kuo-Chen Chou, Yu-Dong Cai
Jul 1, 2006·Biochemical and Biophysical Research Communications·Kuo-Chen Chou, Hong-Bin Shen
Apr 17, 2007·Biochemical and Biophysical Research Communications·Kuo-Chen Chou, Hong-Bin Shen
Aug 19, 2007·Analytical Biochemistry·Kuo-Chen Chou, Hong-Bin Shen
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Citations

Jun 24, 2016·Bioinformatics·Wang-Ren QiuKuo-Chen Chou
Oct 30, 2016·International Journal of Molecular Sciences·Tzu-Hao Kuo, Kuo-Bin Li
Feb 18, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Shu-Feng Zhou, Wei-Zhu Zhong
Mar 24, 2017·Briefings in Bioinformatics·Jian Zhang, Lukasz Kurgan
Feb 1, 2017·Journal of Theoretical Biology·Priyadarshini P PaiSukanta Mondal
Jan 26, 2016·Journal of Theoretical Biology·Jianhua JiaKuo-Chen Chou
Feb 16, 2019·Journal of Computational Chemistry·Sandra Romero-MolinaElsa Sanchez-Garcia
Oct 28, 2019·Current Topics in Medicinal Chemistry·Kuo-Chen Chou
Mar 5, 2016·Oncotarget·Wei ChenKuo-Chen Chou
Aug 19, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yan-Bin WangHai-Cheng Yi
Jun 20, 2020·Evolutionary Bioinformatics Online·Ji-Yong AnYu-Jun Zhao
Apr 12, 2019·Frontiers in Microbiology·Xiaoqing RuChunyu Wang
Mar 15, 2020·Interdisciplinary Sciences, Computational Life Sciences·Yashuang MuXiaodong Liu
Sep 26, 2019·Combinatorial Chemistry & High Throughput Screening·Yi-Heng ZhuDong-Jun Yu

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Software Mentioned

PseAAC
PSAIA
DSSP
- General
iPPBS
propy
Opt
Builder

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