Station1 Frontiers Fellowship Students 2023

17 Aug 2023

MDAnalysis is excited to to have participated this year as a host organization for the Station1 Frontiers Fellowship program for the first time. We thank Station1 for supporting two outstanding students, John Ong and Karen Bekhazi, who have been working with us to understand the evolution of heterogeneity between objects in the Protein Data Bank (PDB) PDBx/mmCIF file format. John and Karen’s research will help inform MDAnalysis’s planned extension of interoperability between MDAnalysis and the PDBx/mmCIF format. Keep reading to learn more about John and Karen’s experience, and download their capstone poster here.

John Ong

Hello everyone, my name is John Ong, and I was one of the Station1 interns working with MDAnalysis this summer. I am a soon-to-be third-year undergraduate student at the University of Utah studying mathematics and computer science.

MDAnalysis is used widely in the biomolecular sciences and thus is important in research that ultimately aims at improving human health. The PDB is an international repository for experimentally-determined 3D structures of biomolecules, such as proteins and nucleic acids. However, data representation techniques for structures on the PDB often differ, despite the same master format (PDBx/mmCIF). Hence, there exists “dialects” within the PDB’s files.

This summer, Karen and I explored the reasons for the existence of these dialects. Through literature reviews and interviews we’ve carried out with both key members within the PDB and PDB user(s), we’ve found experimental methods, knowledge of proteins, data processing methods, and user error to be the most common contributors to these dialects. We also studied the motivations for format changes and regulations (and the lack thereof) within the PDB and its user base.

All in all, this was a rewarding summer. While we did not achieve as many technical results as we would have liked, studying change has been interesting. I’m honored to have been a mentee of @richardjgowers and @hmacdope, and to have had the support of MDAnalysis and its community this summer.

You can find me on GitHub, LinkedIn and my website!

I hope to be able to continue contributing to this incredible community!

Karen Bekhazi

Molecular dynamics simulations are capable of generating new trajectory analyses in their own specific output format. This consequently challenges the tools’ further development and widespread use since they are limited to specific formats that can’t be accessed by all users. This summer, our work has mostly focused on the effects of the lack of a standardized format on molecular dynamics’ scientific and social impact. We evaluated the creation of different PDB file formats by drawing parallels between them and notions in the field of linguistics, such as dialects and stemmatics. Our research was also supported by further study of both the PDB and MDAnalysis’s stakeholders.

I am a rising junior at Smith College. I am studying Engineering Sciences and Chemistry, with an interest in biochemistry, biomaterials, and the intersection of biophysics and chemistry. Originally from Beirut, Lebanon, I enjoy running, reading, and watching movie commentaries in my free time.

Here are my LinkedIn and GitHub profiles.

Thank you to the amazing MDAnalysis community and to our mentors, @richardjgowers and @hmacdope, for this summer!