2021
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Meeko is an AI that helps you improve your skills in League of Legends with personalized coaching, draft suggestions, matchup advice and more. Available on Discord, Windows and macOS, Meeko can also summarize your sessions, protect you from losses and praise your progress.
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Meet Meeko, your new AI Coach for League of Legends. Receive...
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Meet Meeko, your new AI Coach for League of Legends. Receive personalized coaching, draft suggestions, matchup advice and more. Available 24/7 on Discord, Windows and macOS.
- Overview
- Usage notes
- v0.6.0-alpha.3
- API changes in v0.5
- Dependencies
- Installation (from PyPI)
- Installation (from source)
- Examples using the command line scripts
- Python tutorial
- Possibly useful configurations of MoleculePreparation
Meeko reads an RDKit molecule object and writes a PDBQT string (or file) for AutoDock-Vina and AutoDock-GPU. It converts the docking output to RDKit molecules and SD files, without loss of bond orders.
Meeko is developed by the Forli lab at the Center for Computational Structural Biology (CCSB) at Scripps Research.
Meeko does not calculate 3D coordinates or assign protonation states. Input molecules must have explicit hydrogens.
Sampling of macrocycle conformers (paper) is enabled by default.
This release aims to distribute an enhanced mk_prepare_receptor.py. Some features are still being developed, hence the -alpha suffix in the version. Reactive docking is not working in v0.6.0-alpha, but should be restored soon. Documentation is also work in progress.
Class MoleculePreparation no longer has method write_pdbqt_string(). Instead, MoleculePreparation.prepare() returns a list of MoleculeSetup objects that must be passed, individually, to PDBQTWriterLegacy.write_string().
Argument keep_nonpolar_hydrogens is replaced by merge_these_atom_types, both in the Python interface and for script mk_prepare_ligand.py. The default is merge_these_atom_types=("H",), which merges hydrogens typed "H", keeping the current default behavior. To keep all hydrogens, set merge_these_atom_types to an empty list when initializing MoleculePreparation, or pass no atom types to --merge_these_atom_types from the command line:
•Python (>=3.5)
•Numpy
•Scipy
•RDKit
•ProDy (optionally, for covalent docking)
Conda or Miniconda can install the dependencies:
If using conda, pip installs the package in the active environment.
You'll get the develop branch, which may be ahead of the latest release.
Optionally include --editable. Changes in the original package location take effect immediately without the need to run pip install . again.
1. make PDBQT files
AutoDock-GPU and Vina read molecules in the PDBQT format. These can be prepared by Meeko from SD files, or from Mol2 files, but SDF is strongly preferred.
2. convert docking results to SDF
AutoDock-GPU and Vina write docking results in the PDBQT format. The DLG output from AutoDock-GPU contains docked poses in PDBQT blocks. Meeko generates RDKit molecules from PDBQT files (or strings) using the SMILES string in the REMARK lines. The REMARK lines also have the mapping of atom indices between SMILES and PDBQT. SD files with docked coordinates are written from RDKit molecules.
1. making PDBQT strings for Vina or for AutoDock-GPU
At this point, pdbqt_string can be written to a file for docking with AutoDock-GPU or Vina, or passed directly to Vina within Python using set_ligand_from_string(pdbqt_string). For context, see the docs on using Vina from Python.
2. RDKit molecule from docking results
The length of rdkitmol_list is one if there are no sidechains and only one ligand was docked. If multiple ligands and/or sidechains are docked simultaneously, each will be an individual RDKit molecule in rdkitmol_list. Sidechains are truncated at the C-alpha. Note that docking multiple ligands simultaneously is only available in Vina, and it differs from docking multiple ligands one after the other. Each failed creation of an RDKit molecule for a ligand or sidechain results in a None in rdkitmol_list.
For Vina's output PDBQT files, omit is_dlg=True.
When using Vina from Python, the output string can be passed directly. See the docs for context on the v object.
Here we create an instance of MoleculePreparation that attaches pseudo waters to the ligand (see paper on hydrated docking), keeps macrocycles rigid (generally a bad idea), and keeps conjugated bonds and amide bonds rigid. By default, most amides are kept rigid, except for tertiary amides with different substituents on the nitrogen.
The same can be done with the command line script. Note that indices of the atoms in the SMARTS are 0-based for the Python API but 1-based for the command line script:
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May 22, 2024 · Meeko is a tool that converts RDKit molecules to PDBQT format for AutoDock-Vina and AutoDock-GPU. It also converts docking output to RDKit molecules and SD files, and supports macrocycle sampling and atom typing.
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