Computational Structural Biology Lab

Department of Biotechnology
Indian Institute of Technology Kharagpur

What is "Molecule as Layers"? [Go to application]

  1. Any biological molecule, that can be represented with three dimensional coordinates in space can be viewed as layers of atoms sitting on top of each other.
  2. Layers is the algorithm that works on structure files represented in PDB format.
  3. The above animation shows the molecule peeled into layers.
  4. The protein in the animation is “Carbohydrate recognition domain” (PDB ID: 3ZSJ:A)
  5. This protein is peeled into three layers.
  6. The first structure is the native molecule (From left to right).
  7. The layers that are coming out of these structures are hollow (their inside is empty, unlike the native structure).
  8. Sr is the parameter that will help non-randomly sample the surface of the molecule.
  9. Changing Sr from a default 1.52 Å (angstroms) will result in sampling and “Layers” algorithm will provide you with only one output i.e. the sampled surface (insted of layers, which is default).
  10. Keep on increasing Sr you will get a much coarser version of molecular surface.

[Go to application]