Fig. 4

PDB nodes which enable to fetch and extract various properties of deposited PDB structures: The ‘String Manipulation Node’ accepts a column with PDB IDs listed. The ‘PDB Loader’ node is used to download PDB files specified by an URL path. The ‘PDB Property Extractor’ is used to extract structure title, experimental method, crystal resolution (if applicable), number of models (if applicable), R and Rfree factor (if applicable), space group (if applicable), and further experimental remarks from a PDB cell column. An example output table shows UniProt ID (‘Entry’ column), associated PDB IDs (‘PDB’ column), and experimental method (‘Experimental Method’) used for resolving 3D structures