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Journal of Biomolecular Structure and Dynamics Volume 29, 2012 - Issue 6
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Articles

Predicting protein oxidation sites with feature selection and analysis approach

Shen Niu Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, P.R. China; Shanghai Center for Bioinformation Technology, Shanghai, 200235, P.R. China
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Le-Le Hu Institute of Systems Biology, Shanghai University, Shanghai, 200444, P.R. China
,
Lu-Lu Zheng Shanghai Center for Bioinformation Technology, Shanghai, 200235, P.R. China; Hubei Bioinformatics and Molecular Imaging Key Laboratory, Huazhong University of Science and Technology, Wuhan, 430074, China
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Tao Huang Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, P.R. China; Shanghai Center for Bioinformation Technology, Shanghai, 200235, P.R. China
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Kai-Yan Feng Shanghai Center for Bioinformation Technology, Shanghai, 200235, P.R. China
,
Yu-Dong Cai Institute of Systems Biology, Shanghai University, Shanghai, 200444, P.R. China; Centre for Computational Systems Biology, Fudan University, Shanghai, 200433, P.R. China; Gordon Life Science Institute, San Diego, CA, 92130, USACorrespondence[email protected]
,
Hai-Peng Li CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China
,
Yi-Xue Li Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, P.R. China; Institute of Systems Biology, Shanghai University, Shanghai, 200444, P.R. China
&
Kuo-Chen Chou Gordon Life Science Institute, San Diego, CA, 92130, USA
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Pages 1154-1162 | Received 10 Jul 2011, Published online: 18 Apr 2012

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Kannan Sankar, Kam Hon Hoi, Yizhou Yin, Prasanna Ramachandran, Nisana Andersen, Amy Hilderbrand, Paul McDonald, Christoph Spiess & Qing Zhang. (2018) Prediction of methionine oxidation risk in monoclonal antibodies using a machine learning method. mAbs 10:8, pages 1281-1290.
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Y. Liang, S. Zhang & S. Ding. (2018) Accurate prediction of Gram-negative bacterial secreted protein types by fusing multiple statistical features from PSI-BLAST profile. SAR and QSAR in Environmental Research 29:6, pages 469-481.
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Wang-Ren Qiu, Xuan Xiao, Wei-Zhong Lin & Kuo-Chen Chou. (2015) iUbiq-Lys: prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model. Journal of Biomolecular Structure and Dynamics 33:8, pages 1731-1742.
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Ruifeng Xu, Jiyun Zhou, Bin Liu, Yulan He, Quan Zou, Xiaolong Wang & Kuo-Chen Chou. (2015) Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach. Journal of Biomolecular Structure and Dynamics 33:8, pages 1720-1730.
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K. Artemenko, J. Mi & J. Bergquist. (2015) Mass-spectrometry-based characterization of oxidations in proteins. Free Radical Research 49:5, pages 477-493.
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ShaoPeng Wang, JiaRui Li, Xijun Sun, Yu-Hang Zhang, Tao Huang & Yudong Cai. (2020) Computational Method for Identifying Malonylation Sites by Using Random Forest Algorithm. Combinatorial Chemistry & High Throughput Screening 23:4, pages 304-312.
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Mark A. Messerli & Anyesha Sarkar. (2019) Advances in Electrochemistry for Monitoring Cellular Chemical Flux. Current Medicinal Chemistry 26:26, pages 4984-5002.
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Yunyun Liang & Shengli Zhang. (2019) Identifying DNase I hypersensitive sites using multi-features fusion and F-score features selection via Chou's 5-steps rule. Biophysical Chemistry 253, pages 106227.
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Lei Chen, Yu-Hang Zhang, Xiaoyong Pan, Min Liu, Shaopeng Wang, Tao Huang & Yu-Dong Cai. (2018) Tissue Expression Difference between mRNAs and lncRNAs. International Journal of Molecular Sciences 19:11, pages 3416.
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Yunyun Liang & Shengli Zhang. (2018) Identify Gram-negative bacterial secreted protein types by incorporating different modes of PSSM into Chou’s general PseAAC via Kullback–Leibler divergence. Journal of Theoretical Biology 454, pages 22-29.
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Runtao Yang, Chengjin Zhang, Lina Zhang & Rui Gao. (2018) A Two-Step Feature Selection Method to Predict Cancerlectins by Multiview Features and Synthetic Minority Oversampling Technique. BioMed Research International 2018, pages 1-10.
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ShaoPeng Wang, Deling Wang, JiaRui Li, Tao Huang & Yu-Dong Cai. (2018) Identification and analysis of the cleavage site in a signal peptide using SMOTE, dagging, and feature selection methods. Molecular Omics 14:1, pages 64-73.
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Lei Chen, Shaopeng Wang, Yu-Hang Zhang, Jiarui Li, Zhi-Hao Xing, Jialiang Yang, Tao Huang & Yu-Dong Cai. (2017) Identify Key Sequence Features to Improve CRISPR sgRNA Efficacy. IEEE Access 5, pages 26582-26590.
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Vladimir I. Razinkov & Gerd R. Kleemann. 2017. High-Throughput Formulation Development of Biopharmaceuticals. High-Throughput Formulation Development of Biopharmaceuticals 11 43 .
Elisabetta Gianazza, Chiara Parravicini, Roberto Primi, Ingrid Miller & Ivano Eberini. (2016) In silico prediction and characterization of protein post-translational modifications. Journal of Proteomics 134, pages 65-75.
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Lina Zhang, Chengjin Zhang, Rui Gao & Runtao Yang. (2015) An Ensemble Method to Distinguish Bacteriophage Virion from Non-Virion Proteins Based on Protein Sequence Characteristics. International Journal of Molecular Sciences 16:9, pages 21734-21758.
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Xin Ma & Xiao Sun. (2014) Sequence-based predictor of ATP-binding residues using random forest and mRMR-IFS feature selection. Journal of Theoretical Biology 360, pages 59-66.
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André M.N. Silva, Rui Vitorino, M.Rosário M. Domingues, Corinne M. Spickett & Pedro Domingues. (2013) Post-translational Modifications and Mass Spectrometry Detection. Free Radical Biology and Medicine 65, pages 925-941.
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