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wyji001 / Point-Cloud

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How was the file examples/5c2h_11.09 generated? #1

Closed yipy0005 closed 2 years ago

yipy0005 commented 2 years ago

Hi, I'm interested in using PointCloud to predict binding affinities for a protein of interest and a list of ligands, but I don't understand how was the file examples/5c2h_11.09 generated. Can you let me know the steps?

Thank you!

Xinxinatg commented 2 years ago

@yipy0005 Hi have you figured out the way to preprocess the pdb file? It seems like the author only provide the executable files ./POINTNET, ./POINTNET-2048 and ./POINTNET-atomchannel to process the pdb file but didn't give the details in regards to how to eleminate solvents, metals, and ions as decribed in the manuscript. image

wyji001 commented 2 years ago

Many software or libraries can achieve the function of removing solvents, metals, and ions, and using different software will not have any effect on the results. You can even write a simple script to remove manually

Xinxinatg commented 2 years ago

@wyji001 Thanks for your propt reply and again for your wonderful work! I am now using Protein Preparation Wizard in the Schrodinger suite to remove solvents, metals, and ions

yipy0005 commented 2 years ago

@Xinxinatg I'm using Schrodinger's Protein Prep Wiz too! :D