Identifying protein short linear motifs by position-specific scoring matrix

Chun Fang, Tamotsu Noguchi, Hayato Yamana, Fuzhen Sun

    Research output: Chapter in Book/Report/Conference proceedingChapter

    Abstract

    Short linear motifs (SLiMs) play a central role in several biological functions, such as cell regulation, scaffolding, cell signaling, post-translational modification, and cleavage. Identifying SLiMs is an important step for understanding their functions and mechanism. Due to their short length and particular properties, discovery of SLiMs in proteins is a challenge both experimentally and computationally. So far, many existing computational methods adopted many predicted sequence or structures features as input for prediction, there is no report about using position-specific scoring matrix (PSSM) profiles of proteins directly for SLiMs prediction. In this study, we describe a simple method, named as PSSMpred, which only use the evolutionary information generated in form of PSSM profiles of protein sequences for SLiMs prediction. When comparing with other methods tested on the same datasets, PSSMpred achieves the best performances: (1) achieving 0.03–0.1 higher AUC than other methods when tested on HumanTest151; (2) achieving 0.03– 0.05 and 0.03–0.06 higher AUC than other methods when tested on ANCHOR-short and ANCHOR-long respectively.

    Original languageEnglish
    Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    PublisherSpringer Verlag
    Pages206-214
    Number of pages9
    Volume9713
    DOIs
    Publication statusPublished - 2016

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume9713
    ISSN (Print)03029743
    ISSN (Electronic)16113349

    Fingerprint

    Scoring
    Proteins
    Protein
    Cell signaling
    Prediction
    Computational methods
    Cell
    Protein Sequence
    Computational Methods
    Profile

    Keywords

    • Prediction
    • Protein
    • Short linear motifs

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • Computer Science(all)

    Cite this

    Fang, C., Noguchi, T., Yamana, H., & Sun, F. (2016). Identifying protein short linear motifs by position-specific scoring matrix. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 9713, pp. 206-214). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9713). Springer Verlag. https://doi.org/10.1007/978-3-319-41009-8_22

    Identifying protein short linear motifs by position-specific scoring matrix. / Fang, Chun; Noguchi, Tamotsu; Yamana, Hayato; Sun, Fuzhen.

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 9713 Springer Verlag, 2016. p. 206-214 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9713).

    Research output: Chapter in Book/Report/Conference proceedingChapter

    Fang, C, Noguchi, T, Yamana, H & Sun, F 2016, Identifying protein short linear motifs by position-specific scoring matrix. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 9713, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9713, Springer Verlag, pp. 206-214. https://doi.org/10.1007/978-3-319-41009-8_22
    Fang C, Noguchi T, Yamana H, Sun F. Identifying protein short linear motifs by position-specific scoring matrix. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 9713. Springer Verlag. 2016. p. 206-214. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-41009-8_22
    Fang, Chun ; Noguchi, Tamotsu ; Yamana, Hayato ; Sun, Fuzhen. / Identifying protein short linear motifs by position-specific scoring matrix. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 9713 Springer Verlag, 2016. pp. 206-214 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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