Last updated by: Amir Shahmoradi, 9:36 AM, September 9 2015, iCMB, UT Austin

This folder contains data and structural analysis for 213 monomer enzyme proteins. The ultimate goals of the project are:

    -- 
    
    finding the potential variables that create the observed diversity in the correlations of the structural variables with sequence entropy, for example, the wide range of correlations observed in RSA-seqent or WCN-seqent among different proteins.

Contents/

analysis/
    contains the extensive and comprehensive analysis of relationships of different structural properties with each other and with sequence variability (sequence evolutionary rates and sequence entropy)
    
cluster_analysis/
    contains data and analysis for finding the nearest neighbour distances (nnd) of amino acids in individual proteins, using Voronoi partitioning, also the distribution of sequential side-chain and backbone C_alpha distances in individual proteins.
    
contact_order_definition/
    will eventually contain data and analysis for finding the best and optimal parameter-free definition of Contact Order.

ddG_calculations/
	contains all of the files, scripts, and resulting data from the FoldX ddG calculations

structures/ 
	contains all repaired pdb structures in the data set of Echave et al 2014

manuscript/
    contains the preprints of the manuscripts for publication. The complete versions are currently available on OverLeaf website.
    
rate_calculations/
    contains data and analysis for the calculation of the site-wise evolutionary rates and sequence entropy for all enzyme proteins. This includes all of the files, scripts, and resulting data from the rate4site evolutionary rate calculations
    
wcn_best_definition/
    contains analysis and results for obtaining the best definition of WCN kernel in relation to other structural and sequence quantities, in particular the evolutionary rates and B factors.
    
wcn_definition/
   same as in the directory "wcn_best_definition", but contains older, incomplete, unstructured analysis and results.

properties/
	contains the pdb-specific & residue-specific properties of all pdb structures, each in a single file.