AlphaCutter

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

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How to run AlphaCutter

Step 1 : Clone, create environment.

git clone https://github.com/johnnytam100/AlphaCutter.git

cd AlphaCutter

conda env create -f environment.yml

conda activate AlphaCutter

Step 2 : Copy all PDB files to current directory.

cp (path to your PDB files) ./

Step 3 : Run AlphaCutter.

(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

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Options

• --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 if helix_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 if loop_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.

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AlphaCutter-cleaned SwissProt Protein Structures

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

Step 2: Run the following

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