LigExtract: Automated Ligand Indentification and Extraction from PDB Structures

Software that allows large-scale ligand extraction from UniProt ID queries.

Developed by Natália Aniceto (ORCID 0000-0001-7039-0022), Nuno Martinho (ORCID 0000-0001-5102-4756) and Rita Guedes (ORCID 0000-0002-5790-9181).

Below is the overall workflow of LigExtract:

Dependencies

LigExtract was developed on Linux and written in Python 3. It requires PyMol to be installed.

Depending on the system, you might have trouble running pymol from within LigExtract's conda env. Once you installed the condda env provided and activated it, you can run the command below to check if pymol can be used properly.

pymol -cq

If this command returns an error indicating that pymol cannot be found, go to the troubleshooting section.

Running LigExtract

1. git clone LigExtract into your home directory. Make ligextract.sh and build_dependencies.sh inside of bin executable (i.e. chmod 755 *.sh). Add path to LigExtract/bin to your $PATH.

2. create a conda environment from ligext_env.yml.

3. cd into your working directory. This is where all PDBs will be downloaded and processed. This directory must contain a file with a name following the format

    <projectname>_uniprot_list.txt

For example, my project is called "myproteins" so the file will be named

    myproteins_uniprot_list.txt

This file will contain a list of uniprot IDs (see example in docs)

4. Build dependencies (one-off downloads):

    build_dependencies.sh

5. Run LigExtract for your query proteins in your *_uniprot_list.txt file (without cleaning-up at the end).

    ligextract.sh -d myproteins -r 3.5 -o cluster -c nan

with clean-up at the end (i.e. removing all *.cif files):

    ligextract.sh -d myproteins -r 3.5 -o filter -c clean

In this example, ligextract will only consider PDBs up to 3.5 Angstrom resolution and will employ the "cluster" mode (i.e., all ligands that survive filtration are kept, even if duplicated)

Notice how "myproteins" is the name provided to the -d argument, as this must correspond to the prefix of the *_uniprot_list.txt file.

Arguments of ligextract.sh:

 -h    usage information
 -d    name of the directory that will be created with all PDBs. This will be the prefix for multiple files.
 -r    maximum PDB resolution accepted
 -o    selected ligand selection mode: can be 'filter' or 'cluster'
 -c    cleaning outcome: 'clean' will delete all *.cif files; 'nan' will keep all *.cif files.

Usage Notes:

• LigExtract will prompt the user to manually reject or accept each of all experiment methods used to obtain the PDBs associated with the uniprot queries.
• LigExtract will bypass entries with no PDB-format file available. Read more on what causes this situation on https://www.rcsb.org/docs/general-help/structures-without-legacy-pdb-format-files. Eventually we plan to accomodate these exceptions but at the moment LigExtract is not capable on handling them.

Troubleshooting

If you cannot run pymol from the command line once LigExtract's environment is activate, you can try these alternative conditions:

1. You should replace cluster_ligands_hierarchical.py inside bin by cluster_ligands_hierarchical_fixPymol.py by simply renaming the first script or moving it out of the bin directory, and removing the "_fixPymol" portion of the second script. In order for cluster_ligands_hierarchical_fixPymol.py to work, you must make sure that source deactivate deactivates LigExtract's environment without reverting into any base environment.

2. If you still have an error when running cluster_ligands_hierarchical.py ("FileNotFoundError: No such file or directory: 'myproteins/pdbs_filtered_chains/PXXXX/aligned'"), try to replace deactivate by {HOME}/anaconda3/bin/deactivate inside that script (3 locations in the script). Note that this command should be used exactly as is, because HOME is already a variable in the python script that grabs your own home path. This is the typical path to the deactivate executable, and if your path is different you must replace it.

3. If you still get that error when running cluster_ligands_hierarchical.py, replace cluster_ligands_hierarchical.py by cluster_ligands_hierarchical_fixPymol_hideconda.py, making sure you rename the second script with the name of the first.

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If you encounter any errors or issues, or if you have any suggestions, please email Natalia Aniceto at: nataliaaniceto[at]ff.ul.pt