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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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Membrane protein #77

Open d-beltran opened 2 years ago

d-beltran commented 2 years ago

Hi,

I have to search pockets in membrane proteins. I don't want mdpocket to find pockets in the membrane. I can't remove the membrane since I don't want mdpocket to find pockets where the membrane is either. Which is the best approach to solve this situation?

I have played with the -c, -k and -a options but I am not sure if they work as I need or if they just remove the membrane. It is hard to see by eye since when I run mdpockets with the membrane I also see small pockets between the protein and the membrane.

Thank you for your time :)

pschmidtke commented 2 years ago

Not sure this is somehow possible now. What would be needed is a flag to specify for instance what alpha spheres to drop if they overlap with particular residus / atoms.

Is it a simple POPC membrane or a jolly mix of different lipids?

d-beltran commented 2 years ago

Thank you for your fast reply :)

Is it a simple POPC membrane or a jolly mix of different lipids?

I have to work with both situations

By now, I will run mdpocket without the membrane and then I will find out which grid points are overlapping with the membrane somehow. I look forward to use this new flag.

Cheers