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Discngine / fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
MIT License
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Why are the default parameters different from those published in the paper? #62

Closed qyuan7 closed 3 years ago

qyuan7 commented 3 years ago

Hello fpocket team,

When I run fpocket from the Git repo, I found that some of the default parameters are different from those published in the paper, for example the default minimum and maximum radius values of the alpha sphere are 3.4 and 6.2 Å in the current implementation, while those values were 3.0 and 6.0 as published in the paper. Is there any specific reason for making such changes?

Thanks very much,

Best wishes.

Qi

pschmidtke commented 3 years ago

Hi, since the updates after fpocket 2.0 the clustering algorithm and default parameters changed indeed and a lot of parameters were adapted, also for the druggability estimations.

Hope that helps.

peter

From: Qi Yuan @.> Sent: Wednesday, April 21, 2021 21:26 To: Discngine/fpocket @.> Cc: Subscribed @.***> Subject: [Discngine/fpocket] Why are the default parameters different from those published in the paper? (#62)

Hello fpocket team,

When I run fpocket from the Git repo, I found that some of the default parameters are different from those published in the paper, for example the default minimum and maximum radius values of the alpha sphere are 3.4 and 6.2 Å in the current implementation, while those values were 3.0 and 6.0 as published in the paper. Is there any specific reason for making such changes?

Thanks very much,

Best wishes.

Qi

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