3D structure protein alignment in bio3d
Three-dimensional structural alignments between two molecular models can reveal structural properties that are common or unique to either of the proteins. These can suggest evolutionary or functional commonalities. In this recipe, we’ll look at how to get the alignment of two protein sequences in three dimensions and view them in 3D.
Getting ready
For this recipe, we need to install a sequence aligner. We’ll take advantage of the fact that the msa package comes with a version of MUSCLE and install that. You can also use conda to install it separately.
We will also need to install a viewer. We will use PyMOL, which can be installed into a conda environment as follows:
conda install -c conda-forge -c schrodinger pymol-bundle
We’ll also use the bio3d package and some data files in the rbioinfcookbook package.
How to do it…
We can predict structure by performing the following steps:
- Load the...
