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dptech-corp / Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program
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How to visualize #11

Open subercui opened 1 year ago

subercui commented 1 year ago

Hi, I am new to molecular docking, and uni-dock works so nicely. Thanks for the great work!

My question is how we usually visualize the input and results in 3D. Is there any good tool or tutorial you may suggest? Ideally it can be some python packages.

zhengh96 commented 1 year ago

I'm glad you find Uni-Dock helpful!

For visualizing the input and results in 3D, there are several tools and Python packages available. Here are a few popular ones:

  1. PyMOL: PyMOL is a widely used molecular visualization tool that can be extended with Python scripting. You can find tutorials and documentation on their official website: https://pymol.org/2/ PyMOL can be installed using conda:

    conda install -c conda-forge pymol

  2. NGLview: NGLview is a Python package that allows you to visualize molecular structures and trajectories in Jupyter notebooks. It is an IPython widget that uses the NGL WebGL-based molecular viewer. You can find more information and examples in their GitHub repository: https://github.com/nglviewer/nglview NGLview can be installed using conda:

    conda install -c conda-forge nglview

Happy visualizing!

subercui commented 1 year ago

Thank you so much! This is super helpful. BTW, if not limited to python, is there any other tool you would suggest as a better choice? Or you would think PyMOL would be the go-to option?

zhengh96 commented 1 year ago

PyMOL is indeed a popular and powerful tool for working with molecular structures, and it's widely used in the scientific community. However, there are also other tools that you might consider like VMD (https://www.ks.uiuc.edu/Research/vmd/).

Especially, I would like to recommend Mol Viewer (https://molstar.org/viewer/), a web-based Software-as-a-Service (SaaS) tool for molecular visualization. As a web-based tool, Mol Viewer requires no installation and can be accessed from any device with an internet connection, providing a convenient and flexible solution for your molecular visualization needs.