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.. _colab_examples:
Colab Examples
============
`Google Colaboratory <https://colab.google/>`_ (Colab) is a cloud-based platform that allows users to write and execute Python codes through a browser. Regardless of the user's operating system, Colab provides Linux computing backends and some free GPU access.
The following Colab examples are created to provide **an install-free experience** & **some generalizable workflows** of AutoDock Vina via Google Colab notebooks, which work in a similar manner to `Jupyter Notebooks <https://jupyter.org/>`_, in the pre-configured environment with `Meeko <https://github.com/forlilab/Meeko>`_ for receptor and ligand preparation, and other modules - `RDKit <https://rdkit.org/>`_, `Molscrub <https://github.com/forlilab/molscrub>`_, `ProDy <http://www.bahargroup.org/prody/>`_, `reduce2 <https://github.com/cctbx/cctbx_project/tree/master/mmtbx/reduce#reduce2>`_ (formerly `reduce <https://github.com/rlabduke/reduce>`_), and `py3Dmol <https://github.com/avirshup/py3dmol>`_ - for conformer generation, manipulation & pre-processing of protein structures and visualization.
**Subscription is NOT required to run these Colab examples.** Additionally, the input files for the docking calculations are either directly pulled from open databases or generated from user inputs. With that, one can easily customize the notebooks and reuse the workflow for similar calculations on different biochemical systems.
Overview
------------------------
**General Workflow of Docking Calculations in Examples**
.. image:: images/docking_workflow.png
:alt: docking workflow
:width: 100%
:align: center
*Major Python packages used*
* **RDKit** `https://rdkit.org/ <https://rdkit.org/>`_
* **Molscrub (formerly scrubber)** `https://github.com/forlilab/molscrub <https://github.com/forlilab/molscrub>`_
* **Meeko** `https://github.com/forlilab/Meeko <https://github.com/forlilab/Meeko>`_
* **ProDy** `http://www.bahargroup.org/prody/ <http://www.bahargroup.org/prody/>`_
* **cctbx-base** (for reduce2) `https://github.com/cctbx/cctbx_project <https://github.com/cctbx/cctbx_project>`_
* **py3Dmol** `https://3dmol.org/ <https://3dmol.org/>`_
*Data*
* **Phenix-project/geostd** (for reduce2) `https://github.com/phenix-project/geostd/ <https://github.com/phenix-project/geostd/>`_
Basic docking
------------------------
`Run on Colab! <https://colab.research.google.com/drive/1cHSl78lBPUc_J1IZxLgN4GwD_ADmohVU?usp=sharing>`_
The **basic docking example** is a rewrite based on the original basic docking example. In this example, a small molecule ligand (Imatinib, PDB token `STI <https://www1.rcsb.org/ligand/STI>`_) is docked back to a hollow protein structure of mouse c-Abl (PDB token `1IEP <https://www1.rcsb.org/structure/1IEP>`_) to reproduce the complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses.
Flexible docking
------
`Run on Colab! <https://colab.research.google.com/drive/1cazEckGbvl9huWzpxXpd_Qaj0_NipWcz?usp=sharing>`_
The **flexible docking example** is a rewrite based on the original flexible docking example. In this example, a variant of Imatinib (PDB token `PRC <https://www1.rcsb.org/ligand/PRC>`_) is docked back to a hollow protein structure of mouse c-Abl (PDB token `1FPU <https://www1.rcsb.org/structure/1FPU>`_) to reproduce the complex structure. Additionally, Thr315 is set to be a flexible residue. A docked pose that closely resembles the original position of the ligand and **a flipped Thr315** are expected among the top-ranked poses.
Using AD4SF in Vina
---------------
`Run on Colab! <https://colab.research.google.com/drive/1zoSyID2fSoqGz3Zb1_IatUT2uxZ2mCNZ?usp=sharing>`_
The **using AutoDock4 (AD4) scoring function (SF) example** is a rewrite based on the corresponding part of the original basic docking example. This example conducts the same redocking experiment as in *Basic docking* with the AutoDock4 scoring function instead of Vina. To do this, Autogrid4 is used to compute the grid maps, as an additional step after receptor preparation.
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