DockingProtocol

Repository to create a concrete workflow to work with in drug discovery projects.

For a usage example please go to the examples/ folder where you can see a notebook where of some of the classes and methods of this library are used.

Requirements

Other than the requirements specified at requirements.txt, you should have installed the Schrödinger's suite.

Workflow

graph LR
A[Inhibitors] --> B[LigPrep]
B --> C[Docking]
D[Target] --> C[Docking]
C -- Best poses --> E[PELE]
E --> F[Analysis]

1. Input

Target to inhibit prepared and in format pdb.
Csv file with only SMILES and id of all the inhibitor ligands.

- Module: inputPrepare.py

- Class: InputPreparation

- Methods: setUpLigPrepJob, and setUpQMParametrization

1.1. Ligprep

Generation of tautomers and isomers as well as protonation and 3D conformation of the inhibitor ligands in selected pH +- pH_tolerance.

1.2. QM with Jaguar

In case you want to calculate the RESP charges of a specific ligand the input required is just a pdb of the ligand.

2. Docking

Docking of the inhibitors to the target or rescoring docked poses. You will need a grid file for the Glide dockings. For the analysis you will need experimental data with which compare.

Modules:

dockingJob.py

- Class: DockingJob

- Methods: setGlideDocking, setRdockDockingset, setEquibindDocking, rDockRescore, and glideRescore
dockingAnalysis.py

- Class: DockingAnalyzer

- Methods: glideAnalysis, rdockOutputToDataFrame, and rdockAnalysis

3. PELE

Refinement of the docking pose obtained in the previous step in the pipeline. The best pose is chosen as the isomer of the ligand that has the best docking score according to the docking tool scoring function.

- Module: peleJob.py

- Class: PELEJob

- Methods: setGlideToPELESimulation, setRdockToPELESimulation, setEquibindToPELESimulation, and PELEDownloader.

4. Analysis

Part to analyze the results obtained in the PELE simulations.

- Module: peleAnalysis.py

- Class: PELEAnalyzer

- Methods: experimentalDataCollector, equibindDataTrimming, PELEDataCollector, correlationPlotter, and simulationAnalyzer

ignasipuch/pelevs