Finding_surface_residues
DSSP server
- Input : PDB file (6xlu)
- The output contains a column names ACC. The values in this column is either number of water molecule in contact with the residue*10 or Residue's water exposed surface in .
- The ouput obtained was causing problems when read through R.
- To circumvent this, dssp was installed in the system and the protein stucture files (6xlu.pdb) was used to obtain the dssp file.
dssp 6xlu.pdb 6xlu.dssp
- This dssp file was parsed in R using the function parse.dssp from ptm package.
Get Area server
- Input: PDB file (6xlu)
- The output contains a columns saying if the residue is inside or outside - represented as (i/o)
- The output is displayed on the webpage
- This output was manually copied and was converted into a csv file after doing some text editing. This way the file could be easily read in R
NetSurfP 3.0
- Input: FASTA sequence is submitted
- Output: It gives the solvent accessibility, relative solvent accessibility which based on a treshold of 25% - more than 25% the residue is exposed, less than that the residue is burried.
- The RSA values can be taken from the csv file which could be downloaded from the result site.
Note: A pariwise sequence alignment was done with the uniprot spike sequence and the sequence obtained from the 6xlu structure.
The sequences align fairly well.
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