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We know that software tools like I-tasser etc have a web server and a standalone option too. Is there any difference to protein C-scores or efficiency or accuracy if you do it on standalone instead of web server?

What would be the difference if I use the Web server instead of dedicated server for protein modeling and docking?. Available from: https://www.researchgate.net/post/What_would_be_the_difference_if_I_use_the_Web_server_instead_of_dedicated_server_for_protein_modeling_and_docking [accessed Apr 27, 2017].

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  • $\begingroup$ I don't understand the link to Research Gate. Please explain. $\endgroup$
    – canadianer
    Commented Apr 27, 2017 at 20:20

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There should be no difference in output.*** The big difference is likely going to be in the size of the analysis you can perform, and how fast the analysis is performed. A lot of web-servers have a job size limit to prevent one person from hogging resources unless you buy greater access. On a public web-server, your job is queued with everyone else's. If the server is in high demand, you may have to wait along time for your analysis to kick off.

***: I said there should be no difference in output and that is true if you set up your server the same as the public webserver with the same parameters used for analysis execution. This could be a good or bad thing depending on what you are trying to accomplish. Some public webservices do not give you access to all parameters, so setting up your own may give you the ability to tune your analysis to a greater degree.

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  • $\begingroup$ Good answer, but it could be made better with some references. This community asks that answers cite reputable sources so as to ensure higher quality (and hopefully accurate) answers across the community. Thanks. $\endgroup$
    – theforestecologist ♦
    Commented Apr 27, 2017 at 21:40

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