Scripts to search for specific peptide sequences in the PDB
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matchtopml.py
proteinsearch.py

README.md

proteinsearch

Scripts to search for specific peptide sequences in the PDB. For instance, what if you want to find all english words which appear in the PDB?

This code was written for the analysis at The Structure of Spencer.

Finding matches: proteinsearch.py

Two input files are required:

  1. A query file, giving one word per line
  2. The sequence files, in the form of a PDB tabular report.

For the query file I used the ispell english dictionary from the wordlist project and concatenated all the subdictionaries to allow both British and American spellings. I also used the 1000 most popular male & female baby names from 1986 for variety.

The PDB lets you download a tabular report of any search. I used a search for all structures (100,147 on May 14, 2014), and then generated a report including the sequences. After a few minutes of waiting you get a quoted CSV file. The script relies on the following columns:

1. PDB ID
2. Chain ID
6. Sequence
9. Macromolecular Type (filtered for the string 'Polypeptide(L)')

Yes, fasta files would make more sense. Submit a feature request.

Dependencies

The script uses progressbar unless you use the -q option.

It also relies heavily on the esmre library for fast string searching. It implements the nice Aho-Corasick algorithm to search for all queries simultaneously.

Both dependencies should be easily installed using pip.

Examples

To search for everything in your query file, use the following command

proteinsearch.py --exact --min_len 0 \
    --sort-length -m matches.tsv -c counts.tsv \
    query.txt tabularResults.csv

The --exact and -l 0 parameters tell it to use all input words literally, without any filtering. The -m and -c options give output files. The match file gives the query and PDB ID for all search results. The counts file lists all successful queries and the number of places they matched (may be more than one per PDB). The --sort-length option causes the counts file to output in descending word length, as long words are generally more surprising/interesting.

There are some more options to ease filtering of the query files, since spellcheck libraries contain lots of junk. The --trim option removes possessive suffixes, and the --min_len option ignores short queries (defaults to at least 5 residues).

Finally, what about the 6 letters which don't stand for amino acids? Well, they can be interpretted as ambiguous characters. Thus, the query 'BIT' would match either 'DIT' or 'NIT' (or 'BIT', if the PDB author wasn't sure whether the residue was aspartate or aspagine). This behavior is enabled by default.

proteinsearch.py --max-x=1 --trim \
    -m matches.tsv -c counts.tsv --sort-length \
    query.txt tabularResults.csv

Since 'X' can stand for any letter, the counts were being dominated by queries with lots of 'X', such as 'xxxix' (hey, sometimes you want to spell check roman numerals). So the --max-x option filters these out.

Viewing Results: matchtopml.py

To produce nice figures in pymol, matchtopml.py will create a PyMol script file (.pml) to align all the matches for a particular word. It needs the matches.tsv file from proteinsearch.py, as well as the query you're interested in (probably selected from counts.tsv).

matchtopml.py matches.tsv word > word.pml

You may need to customize the outputPML method to suit your preferences. In addition to commands to fetch files, find the sequence, and align structures, the script also does some extensive visual configuration particular to my pymol setup.

The script relies on the findseq (which you may already have from the Pymol script repository, as well as some custom aliases I use (pretty_protein, color_obj, etc.).