Blogs
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 …
COVID S1RBD interacts …
Why did omicron spread so much faster than earlier SARS-CoV-2 variants? We looked at this at the molecular level: where the spike protein’s receptor-binding domain meets the human ACE2 receptor.
We built models of 14 variants (alpha to omicron BA.5) from PDB structures and ran 100 ns MD …
Deep learning for binding …
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 …