pdb_curation

Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark

Cancer Systems Biology, Health and Technology Department, Section for Bioinformatics, 2800, Lyngby, Denmark

Introduction

pdb_curation is a Snakemake pipeline designed to collect protein structures and ensembles from PDB and process and annotate them in different ways.

Requirements

Required software

The pipeline uses the following Python packages:

• pandas
• pypdb

Input structure

The sole input for this pipeline is a pdbs.csv file that should be located in the same directory as the Snakefile (see example included in the repository). This file should contain the following comma-separated columns:

Column name	Expected content	Example
pdbs	four-letter PDB ID code. Can be upper or lowercase	1AQH
type	denotes if the PDB file contains a protein heterocomplex (complex) or not (free)	free

Output structure

The pipeline considers all the PDB ids in the input csv file and processes them automatically. One folder per PDB ID is created in the current directory and itse content varies depending on whether the PDB contains a single protein or a protein complex.

Here is an example of the output of the pipeline for the 1AQH PDB, a monomeric protein:

1AQH/
├── 1AQH_original.pdb
└── 1AQH_pdbredo.pdb
pdb_methods.csv

• 1AQH/1AQH_original.pdb is the unprocessed pdb file downloaded from the PDB database (https://www.rcsb.org/structure/1AQH).

• 1AQH/1AQH_pdbredo.pdb is the refined and rebuilt PDB structure from the PDB-REDO webserver (e.g. https://pdb-redo.eu/db/1aqh/1aqh_final.pdb)

• pdb_methods.csv is a csv table summary file containing the same information as the input file and more, namely:

Column name	Expected content	Example
pdb	four-letter PDB ID code. Can be upper or lowercase	1AQH
type	denotes if the PDB file contains a protein heterocomplex (complex) or not (free)	free
method	denotes the experimental method used to obtain the structure	X-ray diffraction