Multi-scale Bio-Modeling and Visualization 

CS/CAM/BME 395T - #54303

Modeling group: Models of AChR: 2BG9.PDB, AChE: 1C2B.PDB

Richard Bolkey, William Robins and Vinay Siddavanahalli

Multiple resolution grids: 32³ 64³ 128³

Multiple blobbiness: -2.3, -1.0, -0.5, -0.1

Multiple clusters: atomic, residue

Colored according to: Atoms, residues, chains, active sites

Example:

2BG9.PDB, Colored by chains, 128^3, B = -2.3	2BG9.PDB, Colored by chains, 128^3, B = -0.5
1C2B.PDB, Colored by proteins, 128^3, B = -2.3	1C2B.PDB, Colored by proteins, 128^3, B = -0.5

Molecule Group Requirements

We need to "devise an automatic way of placing" the AchR and AchE in the cell membrane. According to the Project Notes, we require a signed distance volume of the membrane, orientation of the AchR (surface normals of the membrane), and the density of the AchR and AchE. This will require a separate flag for the top surface and the folds on the membrane. Each voxel in the volume should be marked with this flag along with a flags marking containment in the membrane boundary, the volume interval around the membrane surface, the basal lamina, and the synaptic cleft.

Our output will be the membrane with AchR and AchE distributed within/along the membrane surface. We will tag each voxel of the membrane with a list of molecules contained within the voxel and their positional attributes.