MetaScreener (manual)

MetaScreener is a collection of scripts developed in various languages (Shell script, Python, Java, and C) that integrates, among others, docking, similarity, and molecular modelling programs. Through this integration, jobs are sent to Slurm on supercomputers, and the data is processed automatically by sorting it into tables and graphs. It has been developed by the Structural Bioinformatics and High-Performance Computing (BIO-HPC, https://bio-hpc.eu) group at UCAM, Universidad Católica de Murcia.

Installation (choose one)

1. git clone https://github.com/bio-hpc/metascreener.git
2. git clone git@github.com:bio-hpc/metascreener.git
3. gh repo clone bio-hpc/metascreener
4. Download the .zip and unzip it in the supercomputing centres you are going to use

Download the singularity image

Needed to secure compatibility with the HPC cluster.

cd metascreener/

wget --no-check-certificate -r "https://drive.usercontent.google.com/download?id=1L3HZ2l1XARqzEKaV14jToUtUOCmo4OjV&export=download&authuser=1&confirm=t&uuid=0c83343d-17fe-4282-bf07-9a2321537a9a&at=APZUnTW_78yhd6klINcZBOjxIU6g:1706872870521" -O singularity/singularity.zip

unzip singularity/singularity.zip -d singularity/

rm singularity/singularity.zip

Available Techniques

1. Virtual Screening (VS)
2. Blind Docking (BD)

Available Software

Code	Software / Version / Date	Type / Link	Notes / Installation Path
AD	AutoDock Vina 1.1.2 (May 11, 2011)	Open source GitHub	—
GN	Gnina v1.3 (Oct 4, 2024)	Open source GitHub	Download the executable to metascreener/MetaScreener/external_sw/gnina/ and give execution permissions
LF	Lead Finder 2104 build 1 (Apr 18, 2021)	Commercial Academic license	License and software required; copy to metascreener/MetaScreener/external_sw/leadFinder/
LS	LigandScout V4.4.7	Commercial	License and software required; copy to metascreener/MetaScreener/external_sw/ligandScout/
DC	Dragon v6.0.38	Commercial	License and software required; copy to metascreener/MetaScreener/external_sw/dragon/
EO	EON v2.4.2.3	Commercial	License and software required; copy to metascreener/MetaScreener/external_sw/openeye/eon/
RC	ROCS v3.6.1.3	Commercial	License and software required; copy to metascreener/MetaScreener/external_sw/openeye/rocs/
OM	OMEGA v5.0.0.3	Commercial	License and software required; copy to metascreener/MetaScreener/external_sw/openeye/omega/

Additional Commercial software

1. Poseview [Required ChemAxon]: generates publication-quality 2D structure-diagrams of protein-ligand complexes. Copy the software in "metascreener/MetaScreener/external_sw/poseview/" (Settings.pxx is provided). You can get an academic license at https://www.biosolveit.de/free-to-academics/.
2. ChemAxon: It is required in poseview for convert to mol2 format. Copy the software in "metascreener/MetaScreener/external_sw/" You can get an academic license at https://chemaxon.com/academic-license.

ESSENCE-Dock

ESSENCE-Dock can take in docking runs from different algorithms and uses all of the information to rescore the compounds using a consensus-based approach. For more information about ESSENCE-Dock, you check out the manuscript here. To use ESSENCE-Dock, you need to make sure the individual docking calculations used metascreener, finished correctly and contain a Results_scoring.csv. If this is not present, or if you moved the directory you can regenerate the file using:

python MetaScreener/extra_metascreener/used_by_metascreener/get_csv.py <docking directory>

After that, you can use ESSENCE-Dock:

./MetaScreener/extra_metascreener/results/ESSENCE-Dock.sh -f <docking_dir1> <docking_dir2> ... -p <proteinFile> -out <output_dir>

There are many more options (like running using slurm, configuring the amount of cores to run on, ...). For more information, you can also always use the help command (./MetaScreener/extra_metascreener/results/ESSENCE-Dock.sh) or feel free to open a GitHub issue.

extra_metascreener

It is a directory that contains multiple scripts used or related to Metascreener.

It is recommended to use these python scripts with the metascreener singularity image "metascreener/singularity/metascreener.simg". For instance:

singularity exec singularity/metascreener.simg python MetaScreener/extra_metascreener/convert/conv_to.py

convert

• conv_to.py*: Convert molecule folders between sdf, pdb, pdbqt and mol2 formats. *Requires ChemAxom for mol2 conversions
• saltRemover.py [Required ChemAxon]: Remove fragments from mol2 file and prints smi without given elements.
• frament_mol2.sh: Use saltRemover.py with the indicated salt remover by adding molecules to Cl, Br.

launchers

• launcher_bd.sh: Launch Blind Dockings with AutoDock Vina or Lead Finder from a protein directory and a ligand directory.
• launcher_ls.sh: Launch virtual screening with LigandScout for 0 to a given number of omitted features (default 0 to 5).

results

• analyse_residues_plip.py: Script to analyse a set of Blind Docking results by residues.
• cross_list_bd.py: Cluster binding of Blind Docking with different ligands or the same.
• cross_list_vs.py: Cross virtual screening lists with different docking programs.
• join_cl_json_bd_session.py: It makes a PyMol session with the results obtained by cross_list_bd.py.
• join_cl_json_vs_session.py: It makes a PyMol session with the results obtained by cross_list_vs.py
• join_ls_sessions.py: It joins experiments carried out with LigandScout in MetaScreener into a single file to view it in LigandScout and excel. Excel files are generated in .csv and .xlsx.

used_by_metascreener

Scripts used internally by Metascreener to process the results.

utils

• distance_ligand_point-py: Calculate the distance between a ligand and a point.