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osFP: a web server for predicting the oligomeric states of fluorescent proteins
Mahidol Univ, Fac Med Technol, Ctr Data Min & Biomed Informat, Bangkok 10700, Thailand..
Mahidol Univ, Fac Med Technol, Ctr Data Min & Biomed Informat, Bangkok 10700, Thailand..
Mahidol Univ, Fac Med Technol, Ctr Data Min & Biomed Informat, Bangkok 10700, Thailand..
Mahidol Univ, Fac Med Technol, Dept Community Med Technol, Bangkok 10700, Thailand..
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2016 (English)In: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 8, article id 72Article in journal (Refereed) Published
Abstract [en]

Background: Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligomeric states can accelerate the effort of protein engineering efforts of creating monomeric FPs. To the best of our knowledge, this study represents the first computational model for predicting and analyzing FP oligomerization directly from the amino acid sequence. Results: After data curation, an exhaustive data set consisting of 397 non-redundant FP oligomeric states was compiled from the literature. Results from benchmarking of the protein descriptors revealed that the model built with amino acid composition descriptors was the top performing model with accuracy, sensitivity and specificity in excess of 80% and MCC greater than 0.6 for all three data subsets (e.g. training, tenfold cross-validation and external sets). The model provided insights on the important residues governing the oligomerization of FP. To maximize the benefit of the generated predictive model, it was implemented as a web server under the R programming environment. Conclusion: osFP affords a user-friendly interface that can be used to predict the oligomeric state of FP using the protein sequence. The advantage of osFP is that it is platform-independent meaning that it can be accessed via a web browser on any operating system and device. osFP is freely accessible at http://codes.bio/osfp/ while the source code and data set is provided on GitHub at https://github.com/chaninn/osFP/.

Place, publisher, year, edition, pages
2016. Vol. 8, article id 72
Keyword [en]
Fluorescent protein, FP, Green fluorescent protein, GFP, Oligomeric state, Data mining, Web server
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:uu:diva-315076DOI: 10.1186/s13321-016-0185-8ISI: 000391705500001OAI: oai:DiVA.org:uu-315076DiVA: diva2:1073489
Funder
Swedish Research Council, C0610701
Available from: 2017-02-10 Created: 2017-02-10 Last updated: 2018-01-13Bibliographically approved

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Wikberg, Jarl E. S.
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