3D structure protein alignment with 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 an alignment of two protein sequences in three dimensions and view them in 3D-rendering software.

Getting ready

For this section, we need at least two external pieces of software—PyMOL and MUSCLE—a 3D structure-rendering program and a sequence aligner.

MUSCLE can be installed with conda as follows:

conda install -c bioconda muscle 

A version of MUSCLE is installed with the msa package, and bio3d can be referred...