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# Author: Noah Herrington, Ph.D. # Email: [email protected] # This README file explains how to use the useful scripts for AF2-based modeling of kinases # in alternative conformations. ## This repository includes five scripts: ## 1) AlphaFold2_advanced_modified.py ## - Used to run AlphaFold2 predictions of a given kinase ## - Outputs 5 models ## - Initial stages of program running installs extra dependencies and required packages ## - "is_training" set to "True" to enable model dropout ## - Takes two arguments: 1. input fasta file and 2. desired output directory ## - Dependencies: biopython 1.79, jax 0.4.1, tensorflow 2.11.0 ## - Usage: python3 AlphaFold2_advanced_modified.py input_fasta output_dir ## 2) colabfold_alphafold.py ## - Modified version of script from ColabFold repository ## - Allows for output directory argument ## - Dependencies installed by or before running AlphaFold2_advanced_modified.py ## - Replace default script with this one ## 3) AF2_kinase_families_stackedbarplot.py ## - Used to classify models downloaded from the AlphaFold2 Protein Structure Database ## into their respective kinase families ## - Must be used in conjunction with kinfam.csv and output from ## Kincore classifier (https://github.com/vivekmodi/Kincore-standalone) as a csv, ## titled "kinases_classified.csv" ## - Dependencies: matplotlib 3.7.0, numpy 1.23.5, pandas 1.4.4, plotly 5.9.0 ## - Usage: python3 AF2_kinase_families_stackedbarplot.py ## 4) Kincore_ConformationDistribution_Doughnutplot.py ## - Used to generate a doughnut-shaped plot of distribution of AF2-predicted models ## by their conformation ## - Outputs fractions of each conformation to the screen and plotly doughnut plot in browser ## - Dependencies: matplotlib 3.7.0, numpy 1.23.5, pandas 1.4.4 ## - Usage: python3 Kincore_ConformationDistribution_Doughnutplot.py ## 5) MSA_models_Mobitz_plot.py ## - Used to generate plot of models by pseudo-dihedral angles (proposed by Mobitz (2015)), ## which group kinase models by movement of their DFG motif ## - Outputs a saved hi-res image of the plot ## - Allows for input of a chosen MSA depth and projection (3D/2D), where 2D represents the Mobitz ## plot and 3D adds an additional dimension for RMSD with respect to a prototyical DFG-in structure ## - Necessitates having downloaded the PDB structure 1ATP and renamed it ## "1ATP_cAMP-dep_prot_kinase_ATP_DFGin_Reference.pdb" ## - Usage: python3 MSA_models_Mobitz_plot.py ## 6) enrichment.py ## - Used to generate enrichment plot of a series of docked models ## - Allows input of colored curves by MSA Depth, pLDDT Score, or Conformation ## - If coloring by pLDDT Score is desired, requires presence of CSVs containing ## classification of all models at those depths (created with Kincore - Dunbrack Lab) ## - Requires two positional arguments: ## a) Name of the kinase, for which plots are created ## b) Quality by which curves are colored (i.e., msa, plddt, conf) ## - Usage: python3 enrichment.py {a} {b}
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