Data and Code from "Structure-based prediction of Ras-effector binding affinities and design of 'branchegetic' interface mutations"

Data, data generation and data analysis for manuscript "Structure-based prediction of Ras-effector binding affinities and design of ‘branchegetic’ interface mutations", currently available as a preprint here.

Contains the following directories:

01_models: Contains all scripts for model generation and selection, as well as some of the generated and selected models.

01_inputs: The different inputs for the homology modelling pipeline. This includes AlphaFold single and complex templates, PDB templates and sequence alignments.

02_validation: Model generation and initial selection for validation models, based on AF2 single models and PDB complex models.

03_production1: Model generation and initial selection for Ras effector complexes, based on AF2 single models and PDB complex models.

04_production2: Model generation and initial selection for Ras effector complexes, based on AF2 single models and AF2 complex models.

05_selection_optics: Code and analysis for selection by unsupervised learning using OPTICS.

02_selected_models: The three representative models selected for each complex.

03_affinity_prediction: Contains code and data for the prediction of binding affinities for Ras effector complexes.

04_branch_pruning: Contains code and data for branch pruning analysis.

05_systems_analysis: Contains code and data for the analysis of Ras effector systems based on affinities derived from affinity prediction and branch pruning analysis.

06_visualization: Information on where in the raw data the panels for the figures in the manuscript can be found.