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hpatch commands and how to identify patches

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hpatch commands and how to identify patches

Hi everyone!

I would like to determine the hpatch score for proteins to predict the affinity to lignin as described by "Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity" by Sammond et al 2014 and developed hpatch by Jacak et al.

I tried to validate the method by BSA hpatch but it is not worked (the output was 8.0 whilw should be 36).

I also don't know how to obtain the hydrophobic patch area and how to identify it in protein structure.

I will be very glad if anyone could told me what is wrong in my commands:


-in:file:l ~/pdblist2

-database ~/main/database

-score:weights ~/main/database/scoring/weights/design_hpatch.wts

-nstruct 5

-ex1 -ex2 -ex3 -ex4 -no_his_his_pairE -extrachi_cutoff 0

-resfile ~/resfile






Thanks everyone!!


Post Situation: 
Thu, 2021-04-29 04:02
Bianca Oliva