In this project, I developed a new method for detecting hydrogen-bond (H-bond) interactions in ProLIF (Protein-Ligand Interaction Fingerprints). ProLIF, based on RDKit and MDAnalysis, is a python package to calculate protein-biomolecular interactions for an molecular dynamic trajectory. Before this …

Hello, welcome back. I am reaching the end of my GSoC journey (week 12)! In the last blog post, we validated our methods with PLINDER, which is a protein-ligand dataset. This week, on the other hand, we focused on the protein-protein dataset, PINDER, and checked whether we got the same tendency as …

Hello, welcome to blog post on the week 10 of my GSoC journey! From the last blog post, we completed the development of the implicit H-bond interaction class. However, it is not perfect. Before getting this method merged into the main ProLIF, we have to validate our method using the explicit H-bond …

Hi again, I am now in the middle of my GSoC journey. Now, we are going to have the main course: implicit hydrogen bond interactions.

In this blog post, you will know more about why calculating the implicit hydrogen bond interaction is important and how we design the algorithm of implicit hydrogen …

Well, two weeks ago, I developed my protein helper function. Before merging codes into the codespace, I will need to undergo a process “code review”.

During the code review period, the code style will need to be aligned to the main codespace, the file will be organized better, and the …

You may have known that I am a GSoC (Google Summer of Code) contributor in 2025, focusing on “MDAnalysis x ProLIF Project 5: H-Bond interactions from implicit hydrogens” (Intro for this project).

Before developing the main function of calculating implicit H-bond interaction, one …

Google Summer of Code is a global program that connects contributors with open source organizations for 12+ week coding projects guided by mentors.

This year (2025), I am glad to be a contributor in “MDAnalysis x ProLIF Project 5: H-Bond interactions from implicit hydrogens”. It is a …

This is a summary list for my publication and conference, which is updated manually. Click on the project codes (e.g. FASTEVALP) to have a brief understanding of the project.

Publication

2024

5. [ …

[The summary is generated by SciSpace.]
[The image is generated by Stable Diffusion XL 1.0.]

Summary of the Research Paper on SARS-CoV-2 Omicron Variants

• The study investigates the spike protein and hACE2 interface of SARS-CoV-2 omicron variants, focusing on hydrogen bond formation.
• It highlights …

Multiple protein conformations are used to accurately represent binding site structure and dynamics in ensemble docking or de novo drug design. Following conformational selection, these conformations are often generated through molecular dynamics (MD) simulations of the protein in the ligand-free …