xy21hb / metascreener

Collection of scripts that integrates docking, virtual screening, similarity and molecular modeling programs.

MetaScreener

MetaScreener is a collection of scripts developed in different languages (Shell script, Python, Java and C) that integrates, among others, docking, similarity and molecular modeling programs, through which jobs are sent to slurm on supercomputers and the data is processed automatically by sorting it into tables and graphs.

Installation (choose one)

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

Download singularity image

Needed to secure compatibility with all cluster.

cd metascreener/

wget --no-check-certificate -r "https://drive.google.com/u/1/uc?export=download&confirm=TLUF&id=1L3HZ2l1XARqzEKaV14jToUtUOCmo4OjV" -O singularity/singularity.zip

unzip singularity/singularity.zip -d singularity/

rm singularity/singularity.zip

Available Techniques

1. Virtual Screening
2. Blind Docking

Available Software

1. AD AutoDock Vina 1.1.2 (May 11, 2011): Open source. https://github.com/ccsb-scripps/AutoDock-Vina.
2. LF Lead Finder version 2104 build 1, 18 April 2021: Commercial software . License and software required (copy in "metascreener/MetaScreener/external_sw/leadFinder/"). You can get an Academic license in http://www.moltech.ru/leadfinder/versions.html.
3. LS LigandScout V4.4.7: Commercial software. License and software required(copy in "metascreener/MetaScreener/external_sw/ligandScout/").

Aditional 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 in 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 in https://chemaxon.com/academic-license.

extra_metascreener

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

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

singularity exec singularity/metasreener.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: Define saltRemover.py by adding molecules to Cl,Br. Enter separated by commas and without white spaces. Default [Cl,Br].

launchers

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

results

• analyse_residues_plip.py: Script to analyze 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: Find the distance between a ligand and a point.