stru.part | R Documentation |
Carries out a partition of the structural regions of a given protein.
stru.part(pdb, cutoff = 0.25)
pdb |
is either a PDB id, or the path to a pdb file |
cutoff |
accessibility below which a residue is considered to be buried. |
The accessibilities of a residue computed in the complex (ACCc) and in the monomer (ACCm) allow to distinguish four structural regions as follows.
Interior: ACCc < cutoff & (ACCm - ACCc) = 0.
Surface: ACCc > cutoff & (ACCm - ACCc) = 0.
Support: ACCm < cutoff & (ACCm - ACCc) > 0.
Rim: ACCc > cutoff & (ACCm - ACCc) > 0.
Core: ACCm > cutoff & ACCc < cutoff.
A dataframe where each residue is assigned to one of the four structural groups considered.
Juan Carlos Aledo
Levy (2010) J. Mol. Biol. 403: 660-670 (PMID: 20868694).
atom.dpx(), res.dpx(), acc.dssp()
## Not run: stru.part('1u8f')
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