Background

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.

About osFP

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.

Tutorial: Using osFP to predict the oligomeric states of FP

osFP is very simple to use requiring only 3 steps as follows:

1. Prior to performing the prediction, users should wait until the gray box found under the Status/Output heading displays the following message: Server is ready for prediction. Please insert/upload sequence in FASTA format.
2. Paste the input sequences for FP of interest into the input box found below the heading Enter your input sequence(s) in FASTA format. Alternatively, users can choose to upload the input file of such data by clicking on the Choose File button. Click on the Submit button to initiate the prediction process.
3. Prediction results are provided in the gray box found below the Status/Output heading. Users can also download the results as a CSV file for later use.

Setting up your own instance of osFP

1. Before you begin, it is recommended to sign up for DigitalOcean. If sign up via this link, you will be given $10 credit.
2. Install the R software and the RStudio Shiny Server on a Linux server by following excellent tutorials available from DigitalOcean and RStudio.
3. After successful installation, you should be able to go to the default welcome page that is hosted on your computer at the URL http://192.168.1.1:3838/
4. Download the osFP source codes and unzip the contents of the ZIP file to the osFP folder at the following path: /srv/shiny-server/osfp/
5. Make sure that the Shiny Server is up and running by running the command: start shiny-server
6. Your local instance of osFP should be able to run from the URL http://192.168.1.1:3838/osfp/

Launching the osFP on your local computer

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:

shiny::runGitHub('osfp','chaninn')

Prerequisite

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:

install.packages(c('shiny','shinyjs','shinythemes','protr','seqinr','RWeka','markdown'))

osFP Data Set

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.

Example Input Data

An example input data that can be used to test the functionality of osFP is available as a FASTA file on our GitHub repository page.

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.

Read the osFP Paper

If you have any questions or comments about the osFP webserver, please direct them to us at chanin.nan[at]mahidol.edu.