I started off week 5 with the usual 10 am sub group meeting where my grad mentor discussed the projects the members of the subgroup have been working on as well as ideas that could turn into new projects. I decided to try another of the protein/ligand binding site problems - with a different protein and ligand. That required me to make some changes in the test scripts which was cool cause I would be doing that when I get started on trying new test cases.

Figure 1: showing the visualization of a problematic protein binding test case.

I decided to color the protein this time (in purple) and there is no ligand configurations (the ligand is oxygen). I’m glad I did this example because this does not work since most of the protein (purple bulk) is found outside the environment (3D box). Another cool part of the project is seeing the skeleton that guides the robot. I’m not sure if I have talked a little about the planner that builds the roadmap; the planning is skeleton-guided in making the roadmap. The skeleton in this case is just a walkthrough all the empty spaces in the configuration space also called the free C-space. This helps to make the roadmap building faster and easier as it knows just exactly where to make the roadmap. The variables I talked about in the previous blog: clearance, energy, and default. An example skeleton and it’s roadmap are shown below.

Figure 2: showing a skeleton mapping the free space of a protein

Figure 3: showing the constructed roadmap after the skeleton in figure 2.

As can be seen in the two figures above, it looks like the planning is not being guided by the skeleton (evident by the roadmaps built outside the protein and skeleton inside). This issue would be a great place to look into sometime next week. And oh, we had the usual group meeting on Friday and this time, we had a peer review discussion on a paper as well as the usual updates.