REstretto (REuse of sub-STRuctures as an Effective Technique for protein-ligand docking TOol): An virtual screening-oriented protein-ligand docking tool with reuse of fragments

Dockerfile is at .devcontainer/Dockerfile. It explains the requirement and what packages are needed.

• Boost (latest)
• Open Babel 2.4.1
  • OpenBabel 3.x (latest) is not supported.

make all

./atomgrid-gen testdata/testgrid.in       # make atom grid
./conformer-docking testdata/testgrid.in  # execute docking

Each program output progress to log file (not stdout).

Sample Input: testdata/testgrid.in

INNERBOX 10, 10, 10
OUTERBOX 20, 20, 20
BOX_CENTER 0.3826, 81.705, 109.195
SEARCH_PITCH 1, 1, 1
SCORING_PITCH 0.25, 0.25, 0.25
MEMORY_SIZE 8000
RECEPTOR testdata/2HU4_A_r.pdbqt
LIGAND testdata/G39.mol2
LIGAND testdata/conformers.mol2
OUTPUT testdata/G39_docked.sdf
GRID_FOLDER testdata/grid

INNERBOX is a region where the center of a compound will be put in. The larger INNERBOX makes wider search but larger calculation cost.

INNERBOX [X], [Y], [Z]

• X: x-width of innerbox (search grid) [Å]
• Y: y-width of innerbox (search grid) [Å]
• Z: z-width of innerbox (search grid) [Å]

OUTERBOX is a region where all atoms of a compound will be put in.

OUTERBOX [X], [Y], [Z]

• X: x-width of outerbox (atom grid) [Å]
• Y: y-width of outerbox (atom grid) [Å]
• Z: z-width of outerbox (atom grid) [Å]

BOX_CENTER is the center of the INNERBOX and OUTERBOX.

BOX_CENTER [X], [Y], [Z]

• X: x-coordinate of center of the pocket [Å]
• Y: y-coordinate of center of the pocket [Å]
• Z: z-coordinate of center of the pocket [Å]

SEARCH_PITCH is a search interval. Smaller SEARCH_PITCH results in finer search, but takes longer calculation time.

SEARCH_PITCH [X], [Y], [Z]

• X: search pitch of x-direction [Å]
• Y: search pitch of y-direction [Å]
• Z: search pitch of z-direction [Å]

SCORING_PITCH is an scoring interval of atom grids and fragment grids. The finer pitch makes the finer scoring, but takes longer calculation time.

SCORING_PITCH [X], [Y], [Z]

• X: atom grid pitch of x-direction [Å]
• Y: atom grid pitch of y-direction [Å]
• Z: atom grid pitch of z-direction [Å]

It defines how much memory will be dedicated for storing fragment grids.

MEMORY_SIZE [MEM]

• MEM: memory size used for fragment grid [MB]

A receptor (protein) file path.

RECEPTOR [RECEPTOR]

• RECEPTOR: file path of receptor

Ligands (compounds) file pathes.

LIGAND [LIGAND]

• LIGAND: file path of ligand
  • You can specify more than one by multiple lines

File path for docked structures (the 3D-coordinates of compounds are only output).

OUTPUT [OUTPUT]

• OUTPUT: file path of docked structure

A path to directory storing atom grids.

GRID_FOLDER [GRID]

• GRID: directory path of atomgrid

Contributions and suggestions are welcome as well as bug reports. We greatly appreciate if you create a new issue and/or a PR (pull request) for these, especially including examples.

• Yanagisawa K, Kubota R, Yoshikawa Y, Ohue M, Akiyama Y. (in prep)