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Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners

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  • Benjamin A Shoemaker
  • Anna R Panchenko

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  • Benjamin A Shoemaker & Anna R Panchenko, 2007. "Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners," PLOS Computational Biology, Public Library of Science, vol. 3(4), pages 1-7, April.
    • Handle: RePEc:plo:pcbi00:0030043
    DOI: 10.1371/journal.pcbi.0030043
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    1. David Eisenberg & Edward M. Marcotte & Ioannis Xenarios & Todd O. Yeates, 2000. "Protein function in the post-genomic era," Nature, Nature, vol. 405(6788), pages 823-826, June.
    2. Ruedi Aebersold & Matthias Mann, 2003. "Mass spectrometry-based proteomics," Nature, Nature, vol. 422(6928), pages 198-207, March.
    3. Anton J. Enright & Ioannis Iliopoulos & Nikos C. Kyrpides & Christos A. Ouzounis, 1999. "Protein interaction maps for complete genomes based on gene fusion events," Nature, Nature, vol. 402(6757), pages 86-90, November.
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    Cited by:

    1. Guilherme T Valente & Marcio L Acencio & Cesar Martins & Ney Lemke, 2013. "The Development of a Universal In Silico Predictor of Protein-Protein Interactions," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-11, May.
    2. Zhu-Hong You & Keith C C Chan & Pengwei Hu, 2015. "Predicting Protein-Protein Interactions from Primary Protein Sequences Using a Novel Multi-Scale Local Feature Representation Scheme and the Random Forest," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-19, May.
    3. Chuanhua Xing & David B Dunson, 2011. "Bayesian Inference for Genomic Data Integration Reduces Misclassification Rate in Predicting Protein-Protein Interactions," PLOS Computational Biology, Public Library of Science, vol. 7(7), pages 1-10, July.
    4. Wei Zhang & Jia Xu & Yuanyuan Li & Xiufen Zou, 2017. "A new two-stage method for revealing missing parts of edges in protein-protein interaction networks," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-22, May.
    5. Saket Navlakha & Anthony Gitter & Ziv Bar-Joseph, 2012. "A Network-based Approach for Predicting Missing Pathway Interactions," PLOS Computational Biology, Public Library of Science, vol. 8(8), pages 1-13, August.
    6. Vijaykumar Yogesh Muley & Akash Ranjan, 2012. "Effect of Reference Genome Selection on the Performance of Computational Methods for Genome-Wide Protein-Protein Interaction Prediction," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-13, July.
    7. Jana Kludas & Mikko Arvas & Sandra Castillo & Tiina Pakula & Merja Oja & Céline Brouard & Jussi Jäntti & Merja Penttilä & Juho Rousu, 2016. "Machine Learning of Protein Interactions in Fungal Secretory Pathways," PLOS ONE, Public Library of Science, vol. 11(7), pages 1-20, July.
    8. Hai-Bo Zhang & Xiao-Bao Ding & Jie Jin & Wen-Ping Guo & Qiao-Lei Yang & Peng-Cheng Chen & Heng Yao & Li Ruan & Yu-Tian Tao & Xin Chen, 2022. "Predicted mouse interactome and network-based interpretation of differentially expressed genes," PLOS ONE, Public Library of Science, vol. 17(4), pages 1-16, April.
    9. Xinyi Liu & Bin Liu & Zhimin Huang & Ting Shi & Yingyi Chen & Jian Zhang, 2012. "SPPS: A Sequence-Based Method for Predicting Probability of Protein-Protein Interaction Partners," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-6, January.
    10. Saeid Rasti & Chrysafis Vogiatzis, 2019. "A survey of computational methods in protein–protein interaction networks," Annals of Operations Research, Springer, vol. 276(1), pages 35-87, May.

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