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ProBiS-Dock Algorithm

ProBiS-Dock algorithm is a docking algorithm complementary to the ProBiS-Dock Database that treats small molecules and proteins as fully flexible entities and allows conformational changes to both upon ligand binding. A new scoring function composed of a binding site-specific scoring function (ProBiS-Score) and a general statistical scoring function is described. ProBiS-Dock enables rapid docking of small molecules into proteins and has been successfully validated against standard benchmarks.

Publication

Please cite the following paper if you use ProBiS-Dock algorithm in your work:

Janez Konc, Samo Lešnik, Blaž Škrlj, Matej Sova, Matic Proj, Damijan Knez, Stanislav Gobec, Dušanka Janežič. ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison. Journal of Chemical Information and Modeling, 2022, doi: 10.1021/acs.jcim.1c01176

Download

  • Executable of the latest version of the ProBiS-Dock algorithm (Linux 64-bit binary): probisdock
  • Source code of the ProBiS-Dock algorithm (latest release): Insidrug project
  • Our version of the SB2012 cross-docking database used for validation in our paper: probisdock_sb2012.zip (based on the SB2012 database available here)
  • Our version of the DUD-E docking database used for validation in our paper: probisdock_dude.zip (based on the DUD-E database available here)

How To Compile from Source

For instructions on how to compile ProBiS-Dock algorithm from source code on Linux systems (Ubuntu and similar) see the README file in the Insidrug project.

Usage Examples

Dock one ligand to one receptor

To dock a ligand to a receptor download the probisdock executable or compile it from source. Download this example's input files; the input files for receptor, centroids, and template ligands can also be obtained at ProBiS-Dock Database by downloading the 'compound 1' binding site of protein 3max. Make sure probisdock is in your path before you begin.
  1. unzip example1.zip
  2. cd example1
  3. chmod +x PATH_TO_PROBISDOCK/probisdock (only the first time)
  4. probisdock --ligands_file crystal_ligand.mol2 --receptor_file receptor_3max_A_compound_1.pdb.gz --template_ligands_file predicted_ligands_3max_A_compound_1.pdb.gz --centro_file probisdock_centro_3max_A_compound_1.cen.gz
After probisdock finishes successfully, summary of the docking run will be in a 'summary' file and the 3D coordinates of the docked ligand pose(s) in 'docked_complexes' file with scores in the TITLE lines.

Dock multiple ligands to one receptor

To dock multiple ligands to a receptor download the probisdock executable or compile it from source. Download this example's input files; the input files for receptor, centroids, and template ligands can also be obtained at ProBiS-Dock Database by downloading the 'compound 1' binding site of protein 3max. Make sure probisdock is in your path before you begin.
  1. unzip example2.zip
  2. cd example2
  3. chmod +x PATH_TO_PROBISDOCK/probisdock (only the first time)
  4. probisdock --ligands_file actives-hdac2-chunk0.mol2.gz --receptor_file receptor_3max_A_compound_1.pdb.gz --template_ligands_file predicted_ligands_3max_A_compound_1.pdb.gz --centro_file probisdock_centro_3max_A_compound_1.cen.gz
After probisdock finishes successfully, summary of the docking run will be in a 'summary' file and the 3D coordinates of the docked ligand pose(s) will be in 'docked_complexes' file with scores in the TITLE lines.

Dock multiple ligands to multiple(!) receptors

To dock multiple ligands to different binding sites on multiple receptors download the probisdock executable or compile it from source. Download this example's input files; the input files, which consist of three different binding sites on 3max receptor, can also be obtained at ProBiS-Dock Database by downloading all binding sites of protein 3max. Make sure probisdock is in your path before you begin.
  1. unzip example3.zip
  2. cd example3
  3. chmod +x PATH_TO_PROBISDOCK/probisdock (only the first time)
  4. probisdock --ligands_file actives-hdac2-chunk0.mol2.gz --probisdock_db_dir ProBiS-DB-3max
After probisdock finishes successfully, summary of the docking run will be in a 'summary' file and the 3D coordinates of the docked ligand pose(s) will be in 'docked_complexes' file with scores in the TITLE lines.