top of page

Ready to dive into Ligand-Protein Simulation?

The team put together an example code file, which you can play with on Google Colab without logging in or setting anything up. Click the button. 

The video below introduces the concepts in the code, and is useful for both scientists and data scientists.  Enjoy!

What did we learn?

  1. We learned how to prepare a protein-ligand complex for MD simulation: We mastered the essential steps to assemble a protein-ligand complex for simulation, using the interaction between the hypoxia-inducible transcription factor HIF2a and a potent small molecule antagonist as our case study. This process ensured we could correctly assemble the components for an effective MD simulation.

  2. We learned to equilibrate the complex for physiological conditions: We acquired the skills to adjust our simulation to mirror stable temperature and pressure conditions, closely resembling a true physiological environment. This ability is crucial for producing realistic simulation outcomes and deepening our understanding of the biological behaviors of proteins and ligands.

  3. We learned to run a 1-minute simulation and save the trajectory: We learned how to perform a 1-minute MD simulation and save the trajectory, enabling visualization and future analysis. These skills form the basis of our understanding in molecular dynamics simulation, paving the way for more complex studies and applications.

bottom of page