Tool:RUPEE protein structure search
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2.8 years ago
rayoub ▴ 110

We have created one of the best, if not the best, protein structure searches available on the net. It is both fast and accurate. It includes both full-length searches and containment searches. If interested, you can check it out at:

https://ayoubresearch.com

The paper is available at:

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213712

Any suggestions for further improvement would be greatly appreciated.

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It is both fast and accurate.

The paper says:

RUPEE has two modes of operation, fast and top-aligned. Fast mode is significantly faster than all other protein structure searches discussed below but at the expense of accuracy.

Maybe rephrase the description in the post?

Another suggestion: The PDB update date on the website says 8/1/2018. To cater to an international audience, maybe use DD-MMM-YYYY or YYYYMMDD format? Because I'm not sure if 8/1/2018 means the 1st of August (US format) or the 8th of January (rest of the world, almost)

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Thanks for your second suggestion. I was not aware of that.

For the issue of fast and accurate, top-aligned is also fast and this is shown in the Response Times section of the Results. It is shown to be faster than mTM, which up until RUPEE, provided the best response times and accuracy that I can find.

It does show that for larger domain sizes, SSM provides better response times but this is at a very big expense of accuracy. I think if you use RUPEE and compare to other available protein structure searches that allow for uploads and are not pre-calculated, you will find RUPEE top-aligned is the fastest of the bunch and just as accurate as the best available searches.