Welcome to Open-ComBind’s documentation!
Open-Combind is an open-source fork of ComBind. Open-ComBind removes all calls to proprietary software and replaces the docking software GLIDE with GNINA.
Open-ComBind is a molecular docking pipeline that harnesses multiple ligand predictions of a molecular docking software. Open-ComBind allows use of ligands without known docked poses to determine the docked pose of a query ligand. This is done through pairwise featurization of the poses and then minimization of the ComBind likelihood.
First Steps
- Installation
How to install Open-ComBind
- Getting Started
How to run Open-ComBind
User Guide
- Command Line Interface
Basics of Open-ComBind: command line interface
- Protein and Ligand Preprocessing and Docking
Protein-ligand preprocessing and docking
- Docked Pose Featurization
Featurization of docked ligand poses
- Statistics, DensityEstimator, and PosePrediction
Scoring and prediction of top ligand pose
- PyMol Visualization of IFP
Visualization of ligand pose features
- Utility Functions for Open-ComBind
Utilities for Open-ComBind