Global comparative structural analysis of responses to protein phosphorylation

This contains the structures and data used for the structural analysis presented in Global comparative structural analysis of responses to protein phosphorylation (Correa Marrero et al., https://doi.org/10.1101/2024.10.18.617420 ). To summarize:

filtered_df.xlsx: dataset of paired phosphorylated structures and their non-phosphorylated counterparts. Each row contains one such pair.

chains_by_protein.zip: each directory (named with a UniProt ID) contains the used structures that form the basis for the analysis. The structures are in PDB format, in a separate directory for each protein in the dataset. The exception is the annotation_per_psite directory, which contains annotation as a csv file for each phosphosite.

extracted_domains.zip: contains structures of Pfam domains (extracted from the previous dataset) in PDB format. Each filename follows the format {PDB ID}_{Chain ID}_{Pfam domain ID}. The domain_coverage.csv file lists the domain coverage of the structure, as well as its length compared to the whole sequence and the whole structure it was extracted from. These are the structures used for the analysis shown in Fig. 1 f-h.

extracted_pfam_domains.zip: contains structures of a broader set Pfam domain structures (the whole set of Pfam domains found to contain a phosphosite in filtered_df.csv) in PDB format. Each directory (named with the Pfam ID) contains the structures. merged_pfam_data.tsv contains metadata about the structures (structure quality, coverage of the domain structure, phosphosite location...). These are the structures used for the analysis shown in Fig. 2.