Structural_Evolution_OxPhos_Files

Summary of contents:

Summary of contents:

This folder contains all files used for the analyses presented in the paper entitled "Structural Diversity and Evolutionary Constraints of Oxidative Phosphorylation":

• Autosomal_RC_OxPhos_phase3_1kGP_missense.vcf.gz: Compressed VCF file containing OxPhos missense variants.

• OxPhos.annotation.tsv.gz: Compressed tsv file used for variant annotation.

• input.tar.gz: This compressed folder contains the PDB model derived from our refined in silico model (without ligands), as well as tsv files providing the mapping between each chain and its associated subunit.

• IFRs.rds: Resulting S4 object containing IFRs information used in downstream analyses.

• OxPhos.SEPV.values.tsv.gz: Compressed tsv file with min-max normalized SEPV values for OxPhos components across vertebrates, mammals, primates, and humans.

• OxPhos_AM_hotspot_data.tsv.gz: Compressed tsv file with AlphaMissense hotspot values for OxPhos components.

• Clinvar_OxPhos_4_benchmarcking.tsv.gz: Compressed tsv file with labeled missense variants affecting the OxPhos system, sourced from the ClinVar database.

• gnomAD_v3.1.2_mitochondrial_OxPhos_subunits.tsv.gz: Compressed tsv file with missense variants for mtDNA-encoded subunits from the gnomAD v3.1.2 database.

• gnomAD_v3.1.2_nuclear_OxPhos_subunits.tsv.gz: Compressed tsv file with missense variants for nuclear-encoded subunits from the gnomAD v3.1.2 database.

• All_groups_MUSCLE_output_files.tar.gz: Compressed folder containing MUSCLE alignments for OxPhos subunits across vertebrates, mammals, and primates.

• DDG_data.tar.gz: This compressed folder includes the resilience of each protein position to mutations. Analyses were performed using the memprane_predict_ddG.py tool from PyRosetta 4, and the folder contains ddG output for each subunit.

• In_silico_models.tar.gz: Compressed archive containing refined in silico structural models generated with the ROSETTA biomolecular modeling suite.

• Example_files_for_AIM_PPL.tar.gz: Compressed folder containing example files required to run the Allelic Imbalance pipeline.

• Structural_Evolution_OxPhos.tar.gz: Compressed folder containing all code used in this study, available at the GitHub repository:

https://github.com/GENOXPHOS/Structural_Evolution_OxPhos