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This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.

Tam, C., & Iwasaki, W. (2023). AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures. In PROTEOMICS. Wiley.https://doi.org/10.1002/pmic.202300176

git clone https://github.com/johnnytam100/AlphaCutter.gitcd AlphaCutterconda env create -f environment.ymlconda activate AlphaCutter

cp (path to your PDB files) ./

(1) Default Settings

python AlphaCutter_v111.py \  --loop_min 20 \  --helix_min 30 \  --fragment_min 5 \  --domain_min 0 \  --pLDDT_min 0 \  --local_contact_range 5 \  --single_out \  --domain_out

(2) Remove shorter loops and helices

python AlphaCutter_v111.py \  --loop_min 15 \  --helix_min 20 \  --fragment_min 5 \  --domain_min 0 \  --pLDDT_min 0 \  --local_contact_range 5 \  --single_out \  --domain_out

• --loop_min – Min. loop length to be considered as non-globular region. (Default:20. Decrease it to remove shorter loops.) Note: This option is not compulsory ifhelix_min is specified.

• --helix_min – Min. helix length to be considered as non-globular region. (Default:30. Decrease it to remove shorter helices.) Note: This option is not compulsory ifloop_min is specified.

• --fragment_min – Min. domain fragment length to be considered as domain region. (Default:5. Increase it to exclude larger domain fragments.)

• --domain_min – Min. domain length to be output as a domain. (Default:0. Increase it to exclude larger domains in output.)

• --pLDDT_min – Min. average pLDDT of domain residues to be output as a domain (Default:0. Increase it to exclude domains predicted with low pLDDT.)

• --local_contact_range – Distinguish non-local contact and local contact used in defining non-globular loops and helices. Loops and helices forming any non-local contacts will be redirected as domain fragments. (Default:5. Not recommended to change it. If you do, also test with--loop_min and--helix_min.)

• --single_out – Output all domains as a single PDB file.

• --domain_out – Output every non-contacting domain as a separate PDB file.

Step 1: Download all parts files fromhttps://doi.org/10.5281/zenodo.7944483

Step 2: Run the following

cat 20230510_AlphaCutter_cleaned_SwissProt_parts-a? > 20230510_AlphaCutter_cleaned_SwissProt.tar.gztar zxvf 20230510_AlphaCutter_cleaned_SwissProt.tar.gz