GSoC 2025 - MDAnalysis x ProLIF Project 5: H-Bond interactions from implicit hydrogens#

Originally, it is a project management repository for GSoC 2025 - MDAnalysis x ProLIF Project 5: H-Bond interactions from implicit hydrogens. Now, it becomes an user guide for calculating H-bond interactions with implicit hydrogens.

Contributor: Yu-Yuan (Stuart) Yang (@yuyuan871111)

Mentors: Cédric Bouysset (@cbouy, @cbouysset), Valerij Talagayev (@talagayev)

Organization: MDAnalysis

Project outline: link

Project final report: link (README first, if you haven’t checked this yet.)

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Environment installation#

Prerequisite:

  • Recommended Python: 3.11 or above.

  • The python packages are managed with uv. Please follow the official guide to install uv.

Once uv is installed, you can clone our repository and synchronize the environment with below code:

git clone https://github.com/yuyuan871111/GSoC2025_Hbond_PM.git

cd GSoC2025_Hbond_PM

uv sync --python 3.11

Quick start#

Please look at our documentation here.

We have three easy cases to demonstrate how to use our ProteinHelper and ImplicitHBDonor/ImplicitHBAcceptor.

  1. Parse PDB files with non-standard residues with ProteinHelper: notebook.

  2. Compare the experimental and computational structures using ImplicitHBDonor/ImplicitHBAcceptor: notebook.

  3. Validate the implicit H-bond method with the explicit H-bond method: notebook.

    For more analyses for the method validation, you will need to download PLINDER and PINDER dataset and prepare the protonated structures. See here for details.