Superpose with MDAnalysis-style algorithms

by Annie Pham

Introduction to the method

This method reimplements ideas found in MDAnalysis superposition algorithms.

Implementation

All aligners in opencadd are factories to configure the method parameters.

This particular follows MDAnalysis’ tutorials: 1) generating pairwise sequence alignments and 2) matching, i.e., superimposing the structures according to those pairwise alignments.

The algorithm follows these steps:

Sequence alignment – using biotite
Mapping between sequence alignment and residues in the structures – using a modified fasta2select
Structural superposition – using MDAnalysis

Which structures you choose?

6HG4 and 6HG9

Practice

First thing you need to do is to download the proteins and pass them to opencadd. We do that with the Structure objects and the .from_pdbid() class method.

[1]:

from opencadd.structure.core import Structure

structure1 = Structure.from_pdbid("6HG4")
structure2 = Structure.from_pdbid("6HG9")

[4]:

%%time
from opencadd.structure.superposition.engines.mda import MDAnalysisAligner, mda_align
from MDAnalysis.analysis.rms import rmsd
aligner = MDAnalysisAligner(alignment_strategy="global", per_residue_selection="name CA or name CB")
results = aligner.calculate([structure1, structure2])

1 residues in <Universe with 4169 atoms> are missing backbone atoms. If this system was obtained from a larger structure using a selection, consider wrapping such selection with `same residue as (<your original selection>)` to avoid potential matching problems.
CPU times: user 966 ms, sys: 30.2 ms, total: 996 ms
Wall time: 963 ms

Analysis

The metadata dictionary in the results contain information about the initial RMSD.

[5]:

print(f'From RMSD = {results["metadata"]["initial_rmsd"]:.3f}A to optimized RMSD of {results["scores"]["rmsd"]:.3f}A')

From RMSD = 1.589A to optimized RMSD of 1.589A

NGLview

If you have trouble with NGLview, follow this troubleshooting guide.

[6]:

import nglview as nv

view = nv.show_mdanalysis(results["superposed"][0].atoms)
view.add_component(results["superposed"][1].atoms)

view