Oligomerization in fluorescent proteins (FP) hinders their usage as a marker for protein tagging. The problems include but are not limited to abnormal localization, interfering with signaling cascades and disturing the normal function of tagged proteins. The ability to predict the oligomeric state of FP may help facilitate the production of monomeric FP that are beneficial for life science applications.
osFP is a web application for predicting the oligomeric state of FP input sequences as being either monomeric or oligomeric. A simple and intuitive user interface is provided where users need only provide the sequence data (FASTA format) for FP of interest.
osFP is very simple to use requiring only 3 steps as follows:
You can also run your own local version of osFP right on your local computer in an R environment by typing the following one-line code:
Before beginning, please make sure to install the following R packages: shiny, shinyjs and shinythemes, protr, seqinr, RWeka and markdown which can be performed by typing the following commands into an R environment:
The complete osFP data set is available for download as a CSV file on our GitHub repository page. This file is comprised of four columns (spelled exactly as found in the CSV file): (i) Name, (ii) OligomericState, (iii) AminoAcidSequence and (iv) Source.
If you find osFP useful, please consider citing the following:
Simeon S, Shoombuatong W, Anuwongcharoen N, Preeyanon L, Prachayasittikul V, Wikberg JES, Nantasenamat C. osFP: a web server for predicting the oligomeric states of fluorescent proteins. Journal of Cheminformatics 8 (2016) 72. DOI: 10.1186/s13321-016-0185-8.
If you have any questions or comments about the osFP webserver, please direct them to us at chanin.nan[at]mahidol.edu.
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