Get non standard residues#

Identifying non-standard residues in a molecular system.

Many biomolecular structures contain non-standard residues such as modified amino acids or post-translational modifications. The function molsysmt.build.get_non_standard_residues() identifies residues that differ from standard amino acid or nucleotide dictionaries.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.build.get_non_standard_residues().

Basic usage#

Let’s show how this function works using cAMP-dependent protein kinase, PDB entry 1ATP, which MolSysMT ships as a demo system. It carries two post-translational modifications: a phosphothreonine in the activation loop and a phosphoserine in the turn motif.

import molsysmt as msm

from molsysmt import systems

molsys = msm.convert(systems['1ATP']['1atp.pdb'])

We now call molsysmt.build.get_non_standard_residues() to detect any non-standard residues.

The result maps each non-standard residue index to its nearest standard sequence equivalent, not to a chemical repair template. Here TPO (phosphothreonine, residue id 197) maps to THR, and SEP (phosphoserine, residue id 338) maps to SER. Their heavy-atom inventories are assessed by exact component templates in molsysmt.build.get_missing_heavy_atoms(); the standard sequence equivalent does not determine their repair chemistry.

msm.build.get_non_standard_residues(molsys)

{182: 'THR', 323: 'SER'}