Computational Structural Biology Lab
Department of Biotechnology
Indian Institute of Technology Kharagpur
- 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.
- Layers is the algorithm that works on structure files represented in PDB format.
- The above animation shows the molecule peeled into layers.
- The protein in the animation is “Carbohydrate recognition domain” (PDB ID: 3ZSJ:A)
- This protein is peeled into three layers.
- The first structure is the native molecule (From left to right).
- The layers that are coming out of these structures are hollow (their inside is empty, unlike the native structure).
- Sr is the parameter that will help non-randomly sample the surface of the molecule.
- 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).
- Keep on increasing Sr you will get a much coarser version of molecular surface.