GSOCMDAPL
Google Summer of Code …
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 …
![Development Wrap-Up: PINDER validation and Autodock Vina H-bond potential [GSoC 2025 - Week 12]](/images/blog_pics/gsoc-wk-12.png)
Development Wrap-Up: …
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 …
![Validation and Optimization: tuning parameters for the implicit H-bond interaction method using datasets [GSoC 2025 - Week 10]](/images/blog_pics/gsoc-wk-10.png)
Validation and …
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 …
![What is the implicit hydrogen? Why need an additional interaction class? [GSoC 2025 - Week 8]](/images/blog_pics/gsoc-wk-8.png)
What is the implicit …
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 …
![Have a better design of protein helper function during code reviews [GSoC 2025 - Week 6]](/images/blog_pics/gsoc-wk-6.png)
Have a better design of …
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 …
![Protein helper function fixed your bond orders of residues (molecules) [GSoC 2025 - Week 4]](/images/blog_pics/gsoc-wk-4.JPG)
Protein helper function …
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 …
MDAnalysis x ProLIF …
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 …