Computational modelling of linear motif-mediated protein interactions

Kobe, Bostjan and Boden, Mikael (2012) Computational modelling of linear motif-mediated protein interactions. Current Topics in Medicinal Chemistry, 12 14: 1553-1561. doi:10.2174/156802612802652439

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Author Kobe, Bostjan
Boden, Mikael
Title Computational modelling of linear motif-mediated protein interactions
Journal name Current Topics in Medicinal Chemistry   Check publisher's open access policy
ISSN 1568-0266
Publication date 2012-07
Sub-type Critical review of research, literature review, critical commentary
DOI 10.2174/156802612802652439
Open Access Status
Volume 12
Issue 14
Start page 1553
End page 1561
Total pages 9
Place of publication Bussum, Netherlands
Publisher Bentham Science Publishers
Collection year 2013
Language eng
Abstract Chemical information can be used to inform biology through being employed to develop bioinformatic tools. One area where bioinformatic tools are valuable is the study of linear motif-mediated protein interactions. Linear motifs are short sequences found mostly in disordered regions of proteins that function in cellular signaling and regulation, by binding to protein interaction domains or by being the target of post-translational modifications. Linear motifs pose difficulty not only to experimental study, but also computational methods; they are difficult to identify due to their small size; and their binding specificity is affected by several factors acting in concert. We discuss the different ways linear motifs can be represented computationally, and how computational approaches can integrate the different specificity-determining factors. We illustrate these issues on our own work focusing on the use of three-dimensional structural information in predicting protein phosphorylation sites, and the integration of diverse types of data in predicting nuclear localization. Computational approaches will play an increasing role in the future, allowing new relationships and system-wide understanding to be unearthed from the large datasets becoming available through high-throughput studies.
Keyword Computational prediction
Data integration
Linear motif
Peptide:protein interactions
Bioinformatic tools
Computational methods
Nuclear localization
Computational approaches
Eukaryotic linera motifs
Proximal motifs
Post-translational modifications
Constraints extrinsic
Potential therapeutics
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
Collections: Official 2013 Collection
School of Information Technology and Electrical Engineering Publications
School of Chemistry and Molecular Biosciences
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 9 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 10 times in Scopus Article | Citations
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Created: Thu, 15 Nov 2012, 14:52:21 EST by System User on behalf of Institute for Molecular Bioscience