pdb_prot_align documentation

pdb_prot_align is a program written by the Bloom lab to align proteins to Protein Data Bank (PDB) structures.

Making such alignments can be useful when you want to relate the evolutionary information in a protein alignment to the structure of a protein. However, the alignments are often difficult because the sequential numbering of sequences used in bioinformatics can differ from the numbering of the protein structure file. The goal of pdb_prot_align is to simplify reconciliation of this numbering.

You may want to simply run pdb_prot_align via its Command-line interface. However, if you prefer to work within Python you can use the pdb_prot_align package, including the top-level pdb_prot_align.main.run() that mimics the Command-line interface.

As described in the Examples, there are also utilities to make it easy to visualize the results in the context of the protein structures using pymol or nglview.