Computational Structural Biology Lab
Source: http://www.csb.iitkgp.ac.in/applications/mol_layers/about.php Parent: http://www.csb.iitkgp.ac.in/applications/mol_layers/main.php
Department of Bioscience and Biotechnology Indian Institute of Technology Kharagpur
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What is "Molecule as Layers"? [Go to application]
- 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.