Group Meeting 23.1 Summary - TechnionYP5779/SimuMole GitHub Wiki

The subject of the meeting: Summary of Stage A of the yearly project with reference to the molecular dynamics project.

Participants: Elizabeth, Ilanit, Michael, Nitzan, Or and Boaz.

Meeting duration: Half an hour.

The Presentation:

  • link to presentation.

  • Input files:

    • We currently use PDB files, but we should check other molecular structures files formats. The reasons for this are:

      • Other formats may provide us with more information (such as forces and chemical bonds between the atoms).
      • Not all proteins have an appropriate PDB file that can be exported from the RCSB site (like our substrate molecule). We need to check whether in the final stage of the project (when we generalize the simulation for each two proteins) we can still use PDB files or not.

    • We need to investigate the structure of the PDB file, for example: What are the units of the X, Y, Z coordinates? What does the numbering of atoms and amino acids express? Is there anything other than the list of atoms that is relevant to us? etc.

  • Loading PDB file into Unity: Currently, we use Blender to convert the '.pdb' file to '.obj' file, and then we load the '.obj' file into Unity. The problem with this solution is that all the chemical information stored in the PDB file was lost during the blender conversion process. Therefore, we need to find a way to implement the conversion from the PDB file to its graphical representation in such a way that the information about the chemical compositions between the atoms will be preserved.

  • MD Algorithm: The missing part of the algorithm is how to calculate the potential energy of an atom. We need to learn about the chemical bonds and forces between the atoms and how this information can be extracted from the PDB files (or from similar files with different format which more suited to our needs). It has been suggested that instead of looking at the level of the atoms or the protein itself, we look at the level of amino acids that build up the protein.

  • Conclusion: In the current Sprint we mainly focused on research: We learned the client's requirements, looked for suitable technologies, and began to formulate the appropriate MD algorithm for the required simulation.

Github Documentation:

  • We showed how the project was documented in Github : wiki files (pros and cons of technologies, software installation guides, etc.) and open issues.

General Topics:

  • We discussed about the group dynamics as it was in the current Sprint: All the tasks are well documented in Github, we held team meetings more frequently, each member of the team was aware of the tasks of the rest.

  • As mentioned in the Telegram group, each team member should record in Github his activity during the semester and particularly during this Sprint (until tomorrow - 24.1).