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:
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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.