I have forgotten to include the meetings I attend every week but I would remember to from now on. I started off my fourth work week with a biology group meeting where we had updates on some ongoing or upcoming biology projects for the lab. Then a meeting on discussion of the module 2 of the pmpl & motion planning crash course. I moved to the crash course on the project I’m working on: the computational biology module. After which I went to the lab’s gitlab and cloned the repository for my project, mainly the binding sites branch, and tried out a given example - I executed code to produce a roadmap for a protein and it’s ligand. The cool thing about this planning is that there are different variables that can be considered in creating the roadmap: energy, clearance, etc and the roadmaps might or might not be the same as seen in pictures 1 and 3.

Figure 1: showing the visualization of the roadmap constructed.

The black bulk is the protein and the green shows the generated roadmap and if you can see the purple zigzags at the ends of the roadmap are the configurations of the ligand. For the computational biology module, I had to read a paper written by my graduate student mentor and others on the process I just completed to check out, compile and run the code. The images below shows a similar but different side to the picture above.

Figure 2: showing the roadmap and some chosen valid ligand configurations

The image above is the visualization of a query.map file which means that some of the ligand configurations are chosen as start and goal configurations which we would like to find a path to. The colored zigzags are those configurations. This is another of the map roadmaps generated for a different parameter: made it colored for distinction.

Figure 3: showing a roadmap based on another variable.