Currently a postdoc but still learning to do (and having fun with) MD simulation.

I work on multidisciplinary topics from molecular mechanism of biomolecular-ligand interactions, to drug discovery, to material design. In my research I adapt various techniques including classical MD, enhanced sampling methods, bioinformatics, and structure-based tools.

(Feb 2025: Getting busy recently, but I still play when I have time.)

About my profile pic:

Cryo-EM structure of SARS-CoV-2 NSP14-NSP10 (PDB: 7N0D chain CD) superimposed on the X-ray structure of SARS-CoV-1 NSP14-NSP10 complexed with cofactor SAM (PDB: 5C8T chain CD).

Xmas card I made several years ago. Image rendered in UCSF Chimera.

Useful links for small molecule design puzzles:

• Public smallworld search, one of the useful database is "REAL-Database-22Q1-4.5B"
  • Not sure about the search criteria
  • Some of the hits in SW search are not in the compound library, and vice versa
• ZINC20 database and ZINC-22 database
• SwissADME server that tells you if the molecule violates some commonly applied chemical filters.
• Original publication of the PAINS filter: https://pubs.acs.org/doi/abs/10.1021/jm901137j
• (Advanced, it is a python package commonly use in real research) Using RDKit to filter chemical structures https://www.rdkit.org/docs/GettingStartedInPython.html#filtering-molecular-datasets
• Pattern identifier in ZINC (options for PAINS pattern highlight)
• SwissBioisostere server Database with information on replacing fragments attached on your compound and prediction of how it affect molecular properties.
• SwissSimilarity server Search for similar compounds in different database using various 2D and 3D fingerprints.

Disclaimer:

• I'm NOT connected to the Foldit team nor the institutions participating in Foldit / Rosetta development. I'm from a tiny research group located in another part of the world.
• I am not good at drug design, but I'm interested in why it binds.